Commit b4990ec5 authored by Julien GUGLIELMINI's avatar Julien GUGLIELMINI

Improved README

parent 004de44e
# Description
When considering a set of aligned sequences, identical characters can be the result of convergent evolution, or direct ancestry - in that case it's called a synapomorphy.
This scripts aims at finding shared characters inside a multiple sequences alignment irrespective of the evolution of the sequences.
When considering a set of aligned sequences, identical character states can be homoplasic (_i.e._ convergent evolution), or synapomorphic (acquired by descent).
This scripts aims at finding shared character states inside a multiple sequences alignment irrespective of the evolution of the sequences.
It takes as input a fasta file containing aligned sequences, and a list of sequences whose name match those in the alignment.
The output is a list of the shared characters followed by an entropy score - the closest is the score to 1, the more the result is significant.
If the sequences you gave as parameters share a common ancestor, then the output are synapomorphies.
The output is a list of the shared character states followed by an entropy score - the closest is the score to 1, the more the result is significant.
If the sequences you gave as parameters share a common ancestor, then the output are synapomorphies. Otherwise they are homoplasies.
# Installation
Download the file, navigate to its location then type
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