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# paHMM-Gene
paHMM-Gene - pairwise indel rate and dN/dS  estimation using pair hidden Markov models

The sources come with an Eclipse CDT project and a Makefile. The makefile should be good for most of the modern 
x86-based architectures. If your system does not support SSE2, change the compiler flags.

# Documentation 

paHMM-Gene is very easy to use. In most cases all you need is to execute the binary and point it to a 
FASTA file with your sequences 

# Input 

A FASTA file with the sequences. PaHMM-Gene processes the sequences in a pairwise manner. 
If your input contains more than 2 sequences, PaHMM-gene will make pairs out of these sequences. For example for 4 sequences there are 6 possible pair combinations.

# Output

PaHMM-gene outputs the following directly into the console (just like Maffty for example):

Model parameters - kappa (transition to transversion rate ratio), dN/dS (omega), 
indel rate (lambda, relative to substitution rate), indel length distribution parameter (epsilon), 
divergence time (expected number of substitutions per codon), sequence 1 name, sequence 2 name, index of a pair.


# Example 

paHMM-Gene --in my_fasta.fas

will output something like this : 

2.772295	0.174614	0.004690	0.708650	0.598915	ENSMUSP00000024887	ENSP00000002125	0
kappa     dn/ds     lambda    epsilon   time      sequence 1          sequence 2      index

# Getting paHMM-Gene

For best performance we advise to compile paHMM-gene on your computer. 
Simply download the repository (green clone or download button ->  download zip) 
unpack and type make in the root folder where the Makefile is. PaHMM-Gene binary will get created. 

Alternatively you can download the binaries here:

http://goo.gl/b78Lou