As per issue #31 and #57, this new release still incorrectly reports its version. I built v3.3.20180129, and it's reporting 3.3.20180130.

$ wget https://github.com/stephaneguindon/phyml/archive/v3.3.20180129.tar.gz
$ tar -xzf v3.3.20180129.tar.gz
$ cd phyml-3.3.20180129
$ ./configure --enable-phyml
$ make
...
make[2]: Entering directory '/tmp/phyml/phyml-3.3.20180129/src'
...
.: Building [phyml]. Version 3.3.20180130 :.
...
$ src/phyml --version

. Command line: src/phyml --version 

. This is PhyML version 3.3.20180130.

N.B. the inconsistencies within the output of make as well.

Received this error when running cloned phyml from github
phyml -i input.phy -m GTR -v e -a e --r_seed 1181 -b 1000

However, it works without bootstrap
phyml -i input.phy -m GTR -v e -a e --r_seed 1181

Hi

I would like to install phyml into a different directory than src, let's say /opt/PhyML. Even though I have run:

./configure --enable-mpi --enable-phyml --prefix=/opt/PhyML --exec-prefix=/opt/PhyML

it always installs it on src from the source tree dir.

EDIT: did not read I must run make install. After this, it created the directory with the binaries and so.

File https://github.com/stephaneguindon/phyml/blob/master/ChangeLog was commited in 2014 and not changed since. It lists changes to versions 4.1 and 5.0 from 1999 to 2000.

The current PhyML is version 3.3, so this ChangeLog does not make sense.

Sorry for the new issue,
i have done
./autogen.sh
./configure
make
i have this error :
libtool: link: gcc -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o m4.o io.o make.o nexus.o init.o xml.o mixt.o -lm times.o: In functionTIMES_Randomize_Tree_With_Time_Constraints':
times.c:(.text+0x61b1): undefined reference to DATE_Assign_Primary_Calibration' times.c:(.text+0x61b9): undefined reference toDATE_Update_T_Prior_MinMax'
times.c:(.text+0x61c1): undefined reference to DATE_Check_Calibration_Constraints' times.c:(.text+0x61cf): undefined reference toDATE_Check_Time_Constraints'
collect2: error: ld returned 1 exit status
`

in think date.o is missing, i had #include "date.h" inside time.c, but i think something expected in the Makefile...

Hello Stephane,

According to the last documentation,
we've tried to use the new --print_json_trace option introduced in PhyML v3.2.0.

This option seams to be not recognized.
We tried with the executable availble for download
We tried with a build of last sources on Fedora 23

Hi,

i just perform ./configure and i have the following lines at the end :(

sed: can't read ./ltmain.sh: No such file or directory
sed: can't read libtoolT: No such file or directory

I'm definitely missed something, any idea?

Hi,

may be this is related to issue #12. If I try to build Debian packages from the latest release 3.2.20160530 I get:

...
gcc -I. -I.. -D_FORTIFY_SOURCE=2 -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -I/usr/include/libhmsbeagle-1 -lhmsbeagle -ldl -c -o utilities.o utilities.c
utilities.c: In function ‘Swap_Partial_Lk’:
utilities.c:6233:7: error: ‘temp’ undeclared (first use in this function)
temp = b->p_lk_left_idx;
^
utilities.c:6233:7: note: each undeclared identifier is reported only once for each function it appears in
Makefile:1836: recipe for target 'utilities.o' failed
...

I checked the diff of utilities.c but did not found any relevant change regarding the temp variable. I suspect a connection to libhmsbeagle since temp is only used in

ifdef BEAGLE

enclosed parts of the code.

The issue appears with a Git clone from libhmsbeagle from 2015-06-09 as well as 2016-05-25 (I wished they would use properly versioned releases.

Kind regards

    Andreas.

Hi

I try to compile phyml 3.2.20160530 on Linux x86_64, gcc 4.9.1 (openMPI 1.8.1) but it fails:

sh ./autogen.sh
/configure --prefix=<...> --enable-phyml --enable-phytime
make

/bin/sh ../libtool --tag=CC --mode=link gcc -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -o phytime main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o times.o m4.o draw.o rates.o mcmc.o stats.o mg.o tiporder.o io.o make.o mixt.o init.o nexus.o date.o xml.o -lm -lm -ldl
libtool: link: gcc -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -o phytime main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o times.o m4.o draw.o rates.o mcmc.o stats.o mg.o tiporder.o io.o make.o mixt.o init.o nexus.o date.o xml.o -lm -ldl
times.o: In function TIMES_main': times.c:(.text+0x4032): undefined reference toFree_Cseq'
collect2: error: ld returned 1 exit status

with MPI enabled, same kind of issue:
/bin/sh ../libtool --tag=CC --mode=link mpicc -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -o phytime main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o times.o m4.o draw.o rates.o mcmc.o stats.o mg.o tiporder.o io.o make.o mixt.o init.o nexus.o date.o xml.o -lm -lm
libtool: link: mpicc -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -o phytime main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o times.o m4.o draw.o rates.o mcmc.o stats.o mg.o tiporder.o io.o make.o mixt.o init.o nexus.o date.o xml.o -lm
utilities.o: In function Bootstrap_From_String': utilities.c:(.text+0x2c4d1): undefined reference toBootstrap_MPI'
times.o: In function TIMES_main': times.c:(.text+0x407a): undefined reference toFree_Cseq'
collect2: error: ld returned 1 exit status

How to solve this?
Regards

Hi,
A collaborator is confused by the versioning of PhyML, since http://www.atgc-montpellier.fr/phyml/ is showing other information than what github says. The latest version is said to be 3.1 and the source code is available "on request".

Hello,

I use a freshly compiled version of PhyML cloned from the GitHub repository (date: 19/07/15) and enabled the BEAGLE support for speeding up the likelihood calculations.
When running the BEAGLE-enabled PhyML with setting the "Tree topology search operations" to "Best of NNI and SPR" and 5 random starting trees, all of my data sets crash at some point with the following error code:

. Best_move < 0 !
. List size = 2
. 0x12c49c30 0x242d9b0
. 0x12c3c2b0 0x23fdc50
== Err. in file spr.c at line 4166 (function 'Evaluate_List_Of_Regraft_Pos_Triple')

The list size is varying based on the data set and the time when crashing. I cannot reproduce this behaviour when using the example data set delivered with PhyML. But the sample size in my data files is much larger and the alignment length much longer (>300 samples, alignment length > 2,000bp). BEAGLE itself should be the problem because I am able to run BEAST using the same library without any problems.

Is this behaviour due to my data sets (nucleotide alignments with gaps) or due to a bug in PhyML's spr.c?

Thanks in advance for your help,
Alex

In stats.c at line 4704 there is an undefined reference to function 'MIGREP_Is_In_Polygon', which is defined in migrep.c.

Hi, when I run the PhyML 3.2.20160531, I found it didn't work because of the error. (Err. in file lk.c at line 805 (function 'Lk_Core')).
Could you help me solve this problem?

Testing on 64 bit Linux CentOS 6,

$ uname -a
Linux ppserver 2.6.32-642.1.1.el6.x86_64 #1 SMP Tue May 31 21:57:07 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
[buildslave@ppserver Tests]$ arch
x86_64

Latest phyml as of 212563a installed as follows:

git clone https://github.com/stephaneguindon/phyml.git
cd phyml/
./autogen.sh
./configure --prefix=${HOME}
make
make install

$ which phyml
$ phyml --version


. Command line: phyml --version 

. This is PhyML version 3.3.20160829.

Failing example using this test file from the Biopython test suite:

$ curl -L -O https://raw.githubusercontent.com/biopython/biopython/master/Tests/Phylip/interlaced2.phy
$ phyml -i interlaced2.phy -d aa ; echo "Return code $?"


. Command line: phyml -i interlaced2.phy -d aa 





                                 ..........................                                      
 ooooooooooooooooooooooooooooo        CURRENT SETTINGS        ooooooooooooooooooooooooooooooooooo
                                 ..........................                                      

                . Sequence filename:                 interlaced2.phy
                . Data type:                     aa
                . Alphabet size:                 20
                . Sequence format:               interleaved
                . Number of data sets:               1
                . Nb of bootstrapped data sets:          0
                . Compute approximate likelihood ratio test:     yes (aBayes branch supports)
                . Model name:                    LG
                . Proportion of invariable sites:        0.000000
                . Number of subst. rate categs:          4
                . Gamma distribution parameter:          estimated
                . 'Middle' of each rate class:           mean
                . Amino acid equilibrium frequencies:        model
                . Optimise tree topology:            yes
                . Tree topology search:              NNIs
                . Starting tree:                 BioNJ
                . Add random input tree:             no
                . Optimise branch lengths:           yes
                . Optimise substitution model parameters:    yes
                . Run ID:                    none
                . Random seed:                   1472461269
                . Subtree patterns aliasing:             no
                . Version:                   3.3.20160829
                . Byte alignment:                16
                . AVX enabled:                   no
                . SSE3 enabled:                  yes

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. 40 patterns found (out of a total of 131 sites). 

. 120 sites without polymorphism (91.60%).

. Computing pairwise distances...

. Building BioNJ tree...
. First round of optimization...

. Building a list of starting trees...
. Best tree found so far has lnL:      -476.67 (9 more trees to examine)
. Best tree found so far has lnL:      -476.67 (8 more trees to examine)
. Best tree found so far has lnL:      -476.67 (7 more trees to examine)
. Best tree found so far has lnL:      -476.67 (4 more trees to examine)

. Finished building the list of trees. Their scores are given below...
. Tree   1, lnL:         0.00
. Tree   2, lnL:         0.00
. Tree   3, lnL:         0.00
. Tree   4, lnL:         0.00
. Tree   5, lnL:         0.00
. Tree   6, lnL:         0.00Segmentation fault (core dumped)
Return code 139

Originally raised via a failing Biopython unit test, see biopython/biopython#919 and biopython/biopython#921

Hi
I am using the latest version of phyML - phyml-3.2.20160530, and when I run the bootstrap analysis, the outgroup that I specified do not appear as such in the generated trees.

When I provide a regular FASTA file to phyml using -i file.fasta the initial overview printed by the program includes the line

                . Sequence format:                               interleaved

which seems to be wrong. It would be good to fix this because it makes the user wonder if it's just an error in what's being printed in the summary or if phyml really did try to read the FASTA in some interleaved way.

Hello,
I'm exiting with this error when running with bootstraps, but not when running without it.
I'm appending the output infomation in support.
Cheers

. Command line: phyml -i primatesNT.phy -d nt -b 10

                             ..........................

ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo
..........................

    ? Sequence filename:                             primatesNT.phy
    ? Data type:                                     dna
    ? Alphabet size:                                 4
    ? Sequence format:                               interleaved
    ? Number of data sets:                           1
    ? Nb of bootstrapped data sets:                  10
    ? Compute approximate likelihood ratio test:     no
    ? Model name:                                    HKY85
    ? Ts/tv ratio:                                   estimated
    ? Proportion of invariable sites:                0.000000
    ? Number of subst. rate catgs:                   4
    ? Gamma distribution parameter:                  estimated
    ? 'Middle' of each rate class:                   mean
    ? Nucleotide equilibrium frequencies:            empirical
    ? Optimise tree topology:                        yes
    ? Tree topology search:                          NNIs
    ? Starting tree:                                 BioNJ
    ? Add random input tree:                         no
    ? Optimise branch lengths:                       yes
    ? Optimise substitution model parameters:        yes
    ? Run ID:                                        none
    ? Random seed:                                   1515225441
    ? Subtree patterns aliasing:                     no
    ? Version:                                       3.3.20180106
    ? Byte alignment:                                32
    ? AVX enabled:                                   yes
    ? SSE enabled:                                   yes

. 336 patterns found (out of a total of 1500 sites).

. 986 sites without polymorphism (65.73%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 4 MB of memory space.

. Score of initial tree: -6417.69

. Building a list of starting trees (NNI search)...

     ╭─────────────────────────╮
     │   0          -6416.10   │ .
     ├─────────────────────────┤
     │   1          -6416.10   │ .
     ├─────────────────────────┤
     │   2          -6416.10   │
     ├─────────────────────────┤
     │   3          -6416.10   │ .
     ├─────────────────────────┤
     │   4          -6416.10   │ .
     ├─────────────────────────┤
     │   5          -6416.10   │
     ├─────────────────────────┤
     │   6          -6416.10   │ .
     ├─────────────────────────┤
     │   7          -6416.10   │
     ├─────────────────────────┤
     │   8          -6416.10   │
     ├─────────────────────────┤
     │   9          -6416.10   │
     ├─────────────────────────┤
     │  10          -6416.10   │ .
     ├─────────────────────────┤
     │  11          -6416.10   │
     ├─────────────────────────┤
     │  12          -6416.10   │
     ├─────────────────────────┤
     │  13          -6416.10   │
     ├─────────────────────────┤
     │  14          -6416.10   │
     ╰─────────────────────────╯

. Fast optimisation of the best trees (SPR search)...

     ╭─────────────────────────╮
     │   1          -6416.07   │ .
     ╰─────────────────────────╯

. Thorough optimisation of the best trees (SPR search)...

     ╭─────────────────────────╮
     │   1          -6416.07   │ .
     ├─────────────────────────┤
     │   2          -6416.07   │ .
     ╰─────────────────────────╯

. Final optimisation steps...

. Log likelihood of the current tree: -6416.071827.

. Launch bootstrap analysis on the most likely tree...

. Non parametric bootstrap analysis

[Segmentation fault

According to tags, the latest stable release is 3.2.0. However, after installing, the version reported is different.

$ phyml-mpi --version
. command-line: phyml-mpi --version 
. This is PhyML version 20160529.

For package management and users knowing if they were up-to-date, I was wondering if these two could be synchronised, please?

Side effect of 43c4e28 for #39 is a missing #endif,

$ grep "^#if" -c src/interface.c
9
$ grep "^#endif" -c src/interface.c
8

Compilation fails (this is a second call to make where everything up to here compiled fine):

$ make
make  all-recursive
make[1]: Entering directory `/home_local/buildslave/repositories/phyml'
Making all in src
make[2]: Entering directory `/home_local/buildslave/repositories/phyml/src'


.: Building [phyml]. Version 3.3.20160830 :.


gcc  -I. -I..     -Wall -O2  -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized  -MT interface.o -MD -MP -MF .deps/interface.Tpo -c -o interface.o interface.c
interface.c:278:1: error: unterminated #if
make[2]: *** [interface.o] Error 1
make[2]: Leaving directory `/home_local/buildslave/repositories/phyml/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home_local/buildslave/repositories/phyml'
make: *** [all] Error 2

Suggested fix:

$ git diff src/interface.c
diff --git a/src/interface.c b/src/interface.c
index c2eb848..c3eb0ff 100644
--- a/src/interface.c
+++ b/src/interface.c
@@ -285,6 +285,7 @@ void Launch_Interface_Input(option *io)
   strcat(io->out_tree_file,"_phyml_tree.txt");
   strcpy(io->out_lk_file,io->in_align_file);

+#endif

   strcat(io->out_lk_file,"_phyml_lk.txt");

Dear Stephane,

I downloaded the zip file and tried
./configure and then make and got the following error. Do you know how to fix this? Thanks in advance.

I have zsh installed but now it's currently disabled I am using the default terminal in GNOME, Ubuntu 14.04.

andrelo@mentat:/Desktop/OMA/phyml-master$ ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking dependency style of gcc... (cached) gcc3
checking for log in -lm... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking for pdflatex... no
checking for latex... no
configure: WARNING: Documentation will not be built!
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
checking for floor... yes
checking for pow... yes
checking for rint... yes
checking for sqrt... yes
checking for strchr... yes
checking for strstr... yes
configure: "On arch x86_64-unknown-linux-gnu use MSSE = -msse"
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @file support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating doc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
sed: can't read ./ltmain.sh: No such file or directory
sed: can't read libtoolT: No such file or directory
andrelo@mentat:/Desktop/OMA/phyml-master$ make
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /home/andrelo/Desktop/OMA/phyml-master/missing aclocal-1.14
/bin/bash: /home/andrelo/Desktop/OMA/phyml-master/missing: No such file or directory
make: *** [aclocal.m4] Error 127

Hi,

I succesfully install phyml (and phyml-mpi and phyml-beagle) from the v3.2 source. However, phytime give me the follow error. Any idea of what happend?
Thanks,
Christian.

/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -o phytime main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o times.o m4.o draw.o rates.o mcmc.o stats.o mg.o tiporder.o io.o make.o mixt.o init.o nexus.o xml.o phyrex.o -lm -lm
libtool: link: gcc -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -o phytime main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o times.o m4.o draw.o rates.o mcmc.o stats.o mg.o tiporder.o io.o make.o mixt.o init.o nexus.o xml.o phyrex.o -lm
phyrex.o: In function PHYREX_MCMC': phyrex.c:(.text+0xcac4): undefined reference toMCMC_PHYREX_Mu'
phyrex.c:(.text+0xcae4): undefined reference to MCMC_PHYREX_Lbda' phyrex.c:(.text+0xcb04): undefined reference toMCMC_PHYREX_Simulate_Backward'
phyrex.c:(.text+0xcb24): undefined reference to MCMC_PHYREX_Scale_Times' phyrex.c:(.text+0xcb44): undefined reference toMCMC_PHYREX_Prune_Regraft'
phyrex.c:(.text+0xcb64): undefined reference to MCMC_PHYREX_Swap_Disk' phyrex.c:(.text+0xcb84): undefined reference toMCMC_PHYREX_Move_Disk_Updown'
phyrex.c:(.text+0xcba4): undefined reference to MCMC_PHYREX_Indel_Hit' phyrex.c:(.text+0xcbc4): undefined reference toMCMC_PHYREX_Indel_Disk'
phyrex.c:(.text+0xcbe4): undefined reference to MCMC_PHYREX_Radius' phyrex.c:(.text+0xcc24): undefined reference toMCMC_PHYREX_Indel_Hit_Serial'
phyrex.c:(.text+0xcc44): undefined reference to MCMC_PHYREX_Indel_Disk_Serial' phyrex.c:(.text+0xcc64): undefined reference toMCMC_PHYREX_Disk_Given_Ldsk'
phyrex.c:(.text+0xcc84): undefined reference to MCMC_PHYREX_Ldsk_Given_Disk' phyrex.c:(.text+0xcca4): undefined reference toMCMC_PHYREX_Ldsk_And_Disk'
phyrex.c:(.text+0xccc4): undefined reference to MCMC_PHYREX_Ldsk_Multi' phyrex.c:(.text+0xcce4): undefined reference toMCMC_PHYREX_Disk_Multi'
phyrex.c:(.text+0xcd04): undefined reference to MCMC_PHYREX_Lbda_Times' phyrex.c:(.text+0xcd24): undefined reference toMCMC_PHYREX_Lineage_Traj'
phyrex.c:(.text+0xcd44): undefined reference to `MCMC_PHYREX_Simulate_Backward_Plus'
collect2: error: ld returned 1 exit status

Hi,

I get this error while trying to configure:

[brozzal1]$ uname -a
Linux 2.6.18-194.17.4.el5 #1 SMP Mon Oct 25 15:50:53 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
[brozzal1]$ arch
x86_64

[brozzal1]$ ./configure --prefix=/home/brozzal1
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
configure: error: cannot find macro directory `m4'

FYI before I did in my home:

tar -xvzf m4-1.4.17.tar.gz
mv m4-1.4.17 m4
cd m4
./configure --prefix=/home/brozzal1
make
make install

Thank you

Hello again,
Here is an error I am getting after an mpi enable config.
Thanks for any help.
"""
...
mpicc -I. -I.. -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -MT mpi_boot.o -MD -MP -MF .deps/mpi_boot.Tpo -c -o mpi_boot.o mpi_boot.c
mpi_boot.c: In function ‘Bootstrap_MPI’:
mpi_boot.c:210:7: warning: passing argument 2 of ‘Connect_CSeqs_To_Nodes’ from incompatible pointer type [enabled by default]
Connect_CSeqs_To_Nodes(boot_data,boot_tree);
^
In file included from mpi_boot.h:19:0,
from mpi_boot.c:13:
utilities.h:1970:6: note: expected ‘struct option ’ but argument is of type ‘struct t_tree *’
void Connect_CSeqs_To_Nodes(calign *cdata, option *io, t_tree *tree);
^
mpi_boot.c:210:7: error: too few arguments to function ‘Connect_CSeqs_To_Nodes’
Connect_CSeqs_To_Nodes(boot_data,boot_tree);
^
In file included from mpi_boot.h:19:0,
from mpi_boot.c:13:
utilities.h:1970:6: note: declared here
void Connect_CSeqs_To_Nodes(calign *cdata, option *io, t_tree *tree);
^
make[2]: ** [mpi_boot.o] Error 1
make[2]: Leaving directory home/.../bin/phyml-master/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory/home/.../bin/phyml-master'
"""

Just downloaded and unzipped phyml-master.zip, then:

briano - ~/Downloads/phyml-master
5228 > ./configure
configure: error: cannot find install-sh, install.sh, or shtool in "." "./.." "./../.."

Looks like there are some broken links in the directory.

Dear Stephane,
I am trying to install phyml on a linux cluster. I downloaded the zip file via "Clone or download" --> "Download ZIP" option, moved the file to my cluster head node, unzipped and cd to phyml-master directory. When I run:
sh ./autogen.sh
I get the following error:
/usr/bin/perl: symbol lookup error: /share/pkg/perl/5.18.1/lib/5.18.1/x86_64-linux-thread-multi/auto/Fcntl/Fcntl.so: undefined symbol: Perl_xs_apiversion_bootcheck

I have two versions of perl on my cluster (1) perl/5.10.0 installed by default on my head node, (2) But I load and use /share/pkg/perl/5.18.1 from our cluster library (so that I can install perl modules locally).
To me the error seems to be that the Build script is picking the wrong version of perl. I usually can fix this by replacing
#! /usr/bin/perl
with
#! /usr/bin/env perl
in Build.PL etc., but here I am unable to figure out where to specify the perl version to use.
Could you please help me solve this?
Thanks a lot,
-Amit.

Hi, thank you for this very helpful tool.

I am trying to compile Phyml from the sources to generate and use the phyml-mpi version.
When I run the "make" command, it ends up with the following error :

make[2]: LIBTOOL@: Command not found
make[2]: *** [phyml-mpi] Error 127
make[2]: Leaving directory /home/[USERNAME]/bin/phyml/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory/home/[USERNAME]/bin/phyml'
make: *** [all] Error 2

Althought libtools is correctly installed in the machine.
Do you know how one could solve this issue ? Otherwise, isn't it possible to also provide the phyml-mpi binary in the github repository ?
Thank you.

Phyml current trace and stderr are set with non-ascii caracters 'bullet-point', is it possible to remove them from traces ? Just to be sure file could be retrieve without decode / encode problems ?
use '-' instead ?
Many thanxs.
Marc

Hi,

Using PhyML 3.2.20160428, in the *_phyml_ancestral_seq output file, I am getting lots of marginal state probabilities greater than one. Used this command:

phyml -i my.phy -d aa -m LG -f e -v 0 -c 12 -a e -s NNI -o tlr -b 0 --freerates --no_memory_check --ancestral

Hi,

Not sure if this is a bug, or just common practice (and I had no idea), but when I try to initially compile I would get errors:

sed: can't read ./ltmain.sh: No such file or directory
sed: can't read libtoolT: No such file or directory

I saw in the commits you removed ltmain.sh, tried editing files, then googling. Finally figured out that you should run libtoolize in the directory.

Is this the correct procedure? Didn't see anything in the documents, and it seems to be working correctly...just wanted to make sure!

Thanks in advance,

Thaine

Hi

I use source code from master branch (version 3.3.20170117) and phyml, phytime or phyml-mpi compile properly but not phyrex. It returns this error message:

gcc  -I. -I..     -Wall -O2 -march=native -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized  -MT phyrex.o -MD -MP -MF .deps/phyrex.Tpo -c -o phyrex.o phyrex.c
phyrex.c: In function ‘PHYREX_MCMC’:
phyrex.c:1140:7: error: ‘t_mcmc’ has no member named ‘use_data’
   mcmc->use_data         = YES;
       ^
phyrex.c:1296:7: error: ‘t_mcmc’ has no member named ‘use_data’
   mcmc->use_data   = YES; 
       ^
make[2]: *** [phyrex.o] Error 1

Do you know what could cause this?

Regards

Linux 2.6.32 x86_64, gcc 4.9.1

Hi,

I've been trying to build the beagle-enabled version of phyml; I cloned directly from GitHub. I've been getting an error during compilation after launching the command make: the function "temp" seems to be undefined in the file utilities.c at line 6331

$ make
make all-recursive
make[1]: Entering directory '/home/gerard/Desktop/phymlmaster'
Making all in src
make[2]: Entering directory '/home/gerard/Desktop/phymlmaster/src'

.: Building [phyml-beagle]. Version 3.3.20170530 :.

gcc -I. -I.. -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -march=native -I/usr/local/include/libhmsbeagle-1 -L/usr/local/lib -lhmsbeagle -ldl -lstdc++ -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c
mv -f .deps/main.Tpo .deps/main.Po
gcc -I. -I.. -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -march=native -I/usr/local/include/libhmsbeagle-1 -L/usr/local/lib -lhmsbeagle -ldl -lstdc++ -MT utilities.o -MD -MP -MF .deps/utilities.Tpo -c -o utilities.o utilities.c
utilities.c: In function ‘Swap_Partial_Lk’:
utilities.c:6331:7: error: ‘temp’ undeclared (first use in this function)
temp = b->p_lk_left_idx;
^
utilities.c:6331:7: note: each undeclared identifier is reported only once for each function it appears in
Makefile:1710: recipe for target 'utilities.o' failed
make[2]: *** [utilities.o] Error 1
make[2]: Leaving directory '/home/gerard/Desktop/phymlmaster/src'
Makefile:370: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/gerard/Desktop/phymlmaster'
Makefile:311: recipe for target 'all' failed
make: *** [all] Error 2

Is there any way I can fix this?

Thanks,
Gerard

PS. This may be related to issue #35 and issue #12.

I've just git cloned the phyml repo and built both phyml and phyml-mpi following the instructions in the README. This is on x86_64, Redhat Scientific Linux release 7.2 (Nitrogen). When I run either phymly or the MPI version:

$ phyml -i input.fasta -m 012212 -f e -v e -c 4 -a e -b 10

I get an almost-immediate error:

. First round of optimization...
== fact_sum_scale: 1049
== pi: 0.219838
== pi 0: 0.228185
== pi 1: 0.269256
== pi 2: 0.219838
== pi 3: 0.282721
== Numerical precision issue alert.
== File lk.c at line 1472 (function '(null)')

== fact_sum_scale: 1048
== pi: 0.219838
== pi 0: 0.228185
== pi 1: 0.269256
== pi 2: 0.219838
== pi 3: 0.282721
== Numerical precision issue alert.
== File lk.c at line 1472 (function '(null)')

== l=0.000824346 lk=0.219073 dlk=INF d2lk=INF
== Err. in file 'lk.c' (line 833)

and the process exits with status 1.

If I run the pre-compiled binary from http://www.atgc-montpellier.fr/download/binaries/phyml/PhyML-3.1.zip the error does not happen.

I'd like to use the MPI version, but there is no pre-compiled binary for it.

Thanks!

/bin/sh ../libtool  --tag=CC   --mode=link mpicc  -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized    -o phyml-mpi main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o 
simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o m4.o io.o make.o nexus.o init.o xml.o mixt.o date.o mpi_boot.o -lm -lm 
libtool: link: mpicc -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -o phyml-mpi main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o int
erface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o m4.o io.o make.o nexus.o init.o xml.o mixt.o date.o mpi_boot.o  -lm
mpi_boot.o: In function `Bootstrap_MPI':
mpi_boot.c:(.text+0x1d4d): undefined reference to `Free_Cseq'
collect2: error: ld returned 1 exit status
Makefile:1739: recipe for target 'phyml-mpi' failed
make[2]: *** [phyml-mpi] Error 1
make[2]: Leaving directory '/tmp/makepkg/phyml-mpi-git/src/phyml-git/src'
Makefile:401: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/tmp/makepkg/phyml-mpi-git/src/phyml-git'
Makefile:333: recipe for target 'all' failed
make: *** [all] Error 2

Please let me know if you need more information on environment, etc.

As per issue #31, the versioning is still incorrect. I just rebuilt and installed the most recent release, v3.3.20170530, and it's still reporting the build date instead.

$ phyml-mpi --version

. Command line: phyml-mpi --version 

. This is PhyML version 3.3.20170531.

Hi Stephane,

when trying to run ./confphy after doing git clone, I'm getting this error:

gcc -I. -I.. -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -MT mcmc.o -MD -MP -MF .deps/mcmc.Tpo -c -o mcmc.o mcmc.c
mcmc.c: In function ‘MCMC_Complete_MCMC’:
mcmc.c:4499:25: error: ‘t_mcmc’ has no member named ‘num_move_phyrex_multi_traj’
mcmc->move_weight[mcmc->num_move_phyrex_multi_traj] = 0.0;
^
mcmc.c:4500:25: error: ‘t_mcmc’ has no member named ‘num_move_phyrex_flip’
mcmc->move_weight[mcmc->num_move_phyrex_flip] = 0.0;
^
Makefile:1665: recipe for target 'mcmc.o' failed
make[2]: *** [mcmc.o] Error 1
make[2]: Leaving directory '/home/jope/soft/phyml/src'
Makefile:388: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/jope/soft/phyml'
Makefile:319: recipe for target 'all' failed
make: *** [all] Error 2

I'm not sure if it is my fault or there's something funny with the code. Do you have any idea how to solve it?

Thank you.

Hi,

I encountered a problem while installing phyml on Mac OSX 10.10.5.

I cloned from Github, successfully launched the config command. Output:

$ ./configure --enable-phyml
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking build system type... x86_64-apple-darwin14.5.0
checking host system type... x86_64-apple-darwin14.5.0
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking dependency style of gcc... (cached) gcc3
checking for log in -lm... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking for pdflatex... no
checking for latex... no
configure: WARNING: Documentation will not be built!
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
checking for floor... yes
checking for pow... yes
checking for rint... yes
checking for sqrt... yes
checking for strchr... yes
checking for strstr... yes
checking for pkg-config... /opt/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating doc/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands

I then launched make, but I get this error :

make
/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-recursive
Making all in src
.: Building [phyml]. Version 3.3.20170131 :.
gcc  -I. -I..     -Wall -O2 -march=native -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized  -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c
In file included from main.c:13:
In file included from ./spr.h:12:
./utilities.h:32:10: fatal error: 'malloc.h' file not found
#include <malloc.h>
         ^
1 error generated.
make[2]: *** [main.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Any idea of what I did wrong here ?

Thanks for your help,

Roxane

There has been a regression in the automatic output file naming which broke one of the Biopython PhyML wrapper tests - see biopython/biopython#919

Historical behavour as per PhyML 3.1 from the http://www.atgc-montpellier.fr/phyml/download.php website:

$ curl -L -O https://raw.githubusercontent.com/biopython/biopython/master/Tests/Phylip/interlaced2.phy
$ curl -L -O http://www.atgc-montpellier.fr/download/binaries/phyml/PhyML-3.1.zip
$ unzip PhyML-3.1.zip
$ rm -rf  interlaced2.phy_*
$  ./PhyML-3.1/PhyML-3.1_linux64 -i interlaced2.phy -d aa ; echo "Return code $?"
...
Return code 0
$ ls -1 interlaced2.phy*
interlaced2.phy
interlaced2.phy_phyml_stats.txt
interlaced2.phy_phyml_tree.txt

Using PhyML from GitHub as of 03a2597 built from source and installed under $PATH,

$ rm -rf  interlaced2.phy_*
$ phyml -i interlaced2.phy -d aa ; echo "Return code $?"
...
Return code 0
$ ls -1 interlaced2.phy*
interlaced2.phy
interlaced2.phy_phyml_stats
interlaced2.phy_phyml_tree

Notice the .txt extension is missing, appending only _phyml_stats and _phyml_tree to the input filename.

This puzzles me as from reading the code interface.c e.g.

  strcpy(io->out_tree_file,io->in_align_file);
  strcat(io->out_tree_file,"_phyml_tree.txt");

Hi, we ran into a bug from some sources we compiled on 2016-05-30 and recently released to our userbase as part of our Geneious PHYML plugin. It seems that when you specify a custom substitution model when invoking from the command line, the output file xxxx_phyml_stats has some malformed characters where it's meant to list the custom model number. See attached output file, that came from the command:

{...}/phyml_linux_64 --boot_progress_every 1 --{...}/PHYML --datatype nt --sequential --multiple 1 --bootstrap 100 --model 012210 -t e --pinv 0.846 --nclasses 1 --alpha e -o tlr --search NNI

PHYML_phyml_stats.txt

I've tried it with a few different alignments and different substitution model numbers, and it's malformed in each case. We can workaround the bug for now, but I think the problem is somewhere in the output producing code.

Hi
In command line phyml -h with the last commit give a "Erreur de segmentation (core dumped)"
after print the start of help :

-m (or --model) model
model : substitution model name.
- Nucleotide-based models : HKY85 (default) | JC69 | K80 | F81 | F84 | TN93 | GTR | custom ()
() : for the custom option, a string of six digits identifies the model. For instance, 000000
corresponds to F81 (or JC69 provided the distribution of nucleotide frequencies is uniform).
012345 corresponds to GTR. This option can be used for encoding any model that is a nested within GTR.

Erreur de segmentation (core dumped)

I left this comment in the google group, too.

Occasionally I see values of 0 for aBayes branch support. As far as I know the aBayes value for a node should be in the range [0.333..., 1], provided the likelihood of the current node arrangement is higher than (or approx. equal to) the 2 NNI rearrangements. Compute_Likelihood_Ratio_Test in alrt.c has a condition that sets the support value to 0 if all likelihoods are approximately equal (see line 316 in commit 6c6e4ad). Do you think that in the case of aBayes the support value should be calculated as normal, even if the three likelihoods are equal? Or even if ln0 is lower than ln1 or ln2, although in this case the tree topology can be optimised further?

Regards,
Kevin

Hi, is there a way to use anything else than the Phylip format as input alignment for phyml? I find the 10 characters limitation of Phylip very annoying. Thank you for your help.

Hey! Compiling the latest version (396:449M - 20150602) in Ubuntu 14.10 with GCC 4.9.1 results in the following error:

.: Building [phyml]. Version 20150602 :.

/bin/bash ../libtool --tag=CC --mode=link gcc -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o m4.o io.o make.o nexus.o init.o xml.o mixt.o -lm -lm
libtool: link: gcc -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o m4.o io.o make.o nexus.o init.o xml.o mixt.o -lm
mcmc.o: In function MCMC_Copy_To_New_Param_Val': mcmc.c:(.text+0xa44a): undefined reference toMIGREP_Update_Sigsq'
collect2: error: ld returned 1 exit status
Makefile:1560: recipe for target 'phyml' failed
make[2]: *** [phyml] Error 1

Hi,

This is my first ever git clone, so I don't know if this is my error or yours :)

configure: error: cannot find install-sh, install.sh, or shtool in "." "./.." "./../.."

Should this script be in the repo, or is it something that I should have somewhere? I'm on MacOSX v13.4.0 (Mac Mini).

I also have got some error while compiling with mpi enabled.

I did:

./autogen.sh
./configure --enable-mpi
make

Error message:

/bin/bash ../libtool --tag=CC --mode=link mpicc -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -o phyml-mpi main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o m4.o io.o make.o nexus.o init.o xml.o mixt.o mpi_boot.o -lm -lm
libtool: link: mpicc -Wall -O2 -msse -fomit-frame-pointer -funroll-loops -Wempty-body -Wuninitialized -o phyml-mpi main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o mg.o m4.o io.o make.o nexus.o init.o xml.o mixt.o mpi_boot.o -lm
times.o: In function TIMES_Randomize_Tree_With_Time_Constraints': times.c:(.text+0x61be): undefined reference toDATE_Assign_Primary_Calibration'
times.c:(.text+0x61c6): undefined reference to DATE_Update_T_Prior_MinMax' times.c:(.text+0x61ce): undefined reference toDATE_Check_Calibration_Constraints'
times.c:(.text+0x61dc): undefined reference to `DATE_Check_Time_Constraints'
collect2: error: ld returned 1 exit status
Makefile:1721: recipe for target 'phyml-mpi' failed
make[2]: *** [phyml-mpi] Error 1

Do you know how this can be fixed?

Thanks

I want to build a tree using a topological constraint file. However, when PhyML reads my constraint tree file I get the following error: "== Taxon 'X' was not found in sequence file 'X.phyx'. I have double checked that the taxon names in the tree file and the alignment file do indeed match. I don't think it's an issue with length or content of the taxon names since the alignment file worked fine with jModelTest. I've attached the constraint tree and alignment files. Any help would be most appreciated!
-Ann

order_constraint_file.txt

mcra_rep_set_refs_muscle_aligned_trim_edit.phyx.zip

Was the --append option removed? If so, is there any way I can easily put it back? (I'm comfortable with forking and doing the patching myself).

Thanks in advance,

Luiz

Hello,
I'm exiting with this error when running with bootstraps, but not when running without it.
As I saw another similar report , I'm appending the output in support.
Cheers

Command line: phyml -i family539.phy -m GTR -b 100 -a e 

                                 ..........................                                      
 ooooooooooooooooooooooooooooo        CURRENT SETTINGS        ooooooooooooooooooooooooooooooooooo
                                 ..........................                                      

                . Sequence filename:				 family539.phy
                . Data type:					 dna
                . Alphabet size:				 4
                . Sequence format:				 interleaved
                . Number of data sets:				 1
                . Nb of bootstrapped data sets:			 100
                . Compute approximate likelihood ratio test:	 no
                . Model name:					 GTR
                . Proportion of invariable sites:		 0.000000
                . Number of subst. rate categs:			 4
                . Gamma distribution parameter:			 estimated
                . 'Middle' of each rate class:			 mean
                . Nucleotide equilibrium frequencies:		 empirical
                . Optimise tree topology:			 yes
                . Tree topology search:				 NNIs
                . Starting tree:				 BioNJ
                . Add random input tree:			 no
                . Optimise branch lengths:			 yes
                . Optimise substitution model parameters:	 yes
                . Run ID:					 none
                . Random seed:					 1496747653
                . Subtree patterns aliasing:			 no
                . Version:					 3.3.20170119
                . Byte alignment:				 16
                . AVX enabled:					 no
                . SSE3 enabled:					 yes

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. 493 patterns found (out of a total of 714 sites). 

. 188 sites without polymorphism (26.33%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 3 MB of memory space.

. First round of optimization...

. Building a list of starting trees...
. Best tree found so far has lnL:     -5355.64 (9 more trees to examine)
. Best tree found so far has lnL:     -5355.50 (8 more trees to examine)

. Finished building the list of trees. Their scores are given below...
. Tree   1, lnL:     -5352.12
. Tree   2, lnL:     -5355.50
. Tree   3, lnL:     -5355.52
. Tree   4, lnL:     -5355.53
. Tree   5, lnL:     -5355.54
. Tree   6, lnL:     -5355.54
. Tree   7, lnL:     -5355.55
. Tree   8, lnL:     -5355.56
. Tree   9, lnL:     -5355.58
. Tree  10, lnL:     -5355.64

. Improving the best trees (5 trees to process)...
. Better tree found so far has lnL:     -5352.11 (5 more trees to examine)

. Improving the best trees using NNIs...
. Better tree found -> lnL:     -5352.11 (5 more trees to examine)

. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -5352.111029.

. Launch bootstrap analysis on the most likely tree...

. Non parametric bootstrap analysis 

  [
== -5388.441785 -- -5388.787903
== Edge: 16
== is_mixt_tree: 0
== Err. in file optimiz.c at line 864 (function '(null)') 

Tried to build phyml on OSX. Unfortuntely, libtoolize is not found on that platform.

However, installing libtool from homebrew (brew install libtool )solves the problem, together with changing line 6 of confphy from libtoolize to glibtoolize.

Maybe add an extra confphy for osx with the file already in, or add a checking step to the script to test which of libtoolize or glibtoolize is available.

Hello,

It seems that there is an incoherence in the way the output filenames are generated depending on how the software is used.

In the interactive interface: https://github.com/stephaneguindon/phyml/blob/master/src/interface.c#L133
the ".txt" suffix is added
while in the command line interface: https://github.com/stephaneguindon/phyml/blob/master/src/cl.c#L1429 it is not.

The manual seems to indicate that the version without the extension is the right one ?

Cheers