nousiaso / catsequences

A tool for concatenating multiple fasta alignments for supermatrix phylogenetic analyses

catsequences

A tool for concatenating multiple fasta alignments for supermatrix phylogenetic analyses

Please reference this DOI:

Usage: catsequences filename

Where filename contains a list of files with sequences to be concatenated The concatenated alignments are outputted to a file called "allseqs.fas" Partition information will be written to the file "allseqs.partitions.txt"

The sequence names are read up to the first "." or "|" (or the end of the name)

---

To install:

Download the file "catsequences.c" and or if you have git installed use the command:

git clone https://github.com/ChrisCreevey/catsequences.git

To build catsequences type:

cc catsequences.c -o catsequences -lm

Copy the executable "catsequences" to somewhere on your path like "~/bin" to have access to it from anywhere.

---

To use:

Usage:

catsequences filename

where filename contains a list of files with sequences to be concatenated

The concatenated alignments are outputted to a file called "allseqs.fas"

Partition information will be written to the file "allseqs.partitions.txt"

The sequence names are read up to the first "." or "|" (or the end of the name)

The easiest way to create the list input file is to use a command like:

ls *.fasta > list

assuming that all your input file have the extension ".fasta"

The software will put in '?' for the entire length of any gene for which the species is missing.