This repository contains my scripts from the /usr/local/bin/my_scripts directory.
Most of the scripts are written in Perl in the good old days.

The following is a brief description of each program (to come)

GenSkewApp.jar
N50
N50.p
README.md
R_skripts
aaRSpplacer
aaRSprofileG
aaRSprofileT
abyss-pe-auto
adaptercleaner
addngs
alignall
alignall.old
aligner
aln2aln
aln2aln.py
bowtie2coverage
cc2ps
cc2ps_editing
codeml.old
count.reads
countseq
do4all
extract_stem-loops
fa2coevol
fasta
fasta2
gb2gor
gb2map
gb2mf
genomestats
get-contigs
get-contigs-org
gname2num.phy, change gene names to numbers in a GO file go2gr
go2nex
go2nex.old
go2nex_out
go2ps
go2ps.old
go2psv
gorcoder
gorcom
gorcom.old
gorcom_previous
gorcom_v1
gornex
gorsim
gotree
helptext.txt
length-hist
make_codon_table
mcons
mcons.old
mf2cc, create a coordinate file or a gene order file from a masterfile.
mf2fasta
mf2fasta.new
mkngs
mpepper, pepper -t on multiple files
mtann, quick annotation of mitochondrial genomes
newalign, program to select, align, and concatenated sequences from individual mitochondrial genes
ntsoapalign
pal2nal
pal2nal_all
paml
parse_codeml
pbdatebars
phylip2fasta
plate
plotcoevoltree
plotcoevoltree.R
puzzleboot
ramdisk
read_paml_rates
remove-small-contigs
rename_trees
renamegb
rmbarcode
rmngs
rmtrees
rmtrees_consel
sauveguard
seq2seq
skiptRNA, a program to convert multiple GO files into a NEXUS file for MPMEMG analysis
soapalign, replaced by newalign; a program to select, align, and concatenated sequences from individual mitochondrial genes
soapalign.mod
soapalign.pretdy
sort-seqs
split2cont
splitGO, a perl script to split a multi-species go file into individual go files (used as input by skiptRNA program) sto2ali
talign
temp
temp.ERR
testal
trimfastq
updategb
updategb2
updatemf