ChrisCreevey / 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)

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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.

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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 " " (space) (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.

Trouble Shooting

If the total concatenated seuquneces length is larger than defined in the code you recieve an ERROR saying:

ERROR: The total concatenated sequence length is greater than the maximum length defined (1000000)!
    To fix this increase the value of MAXLEN on line 15 of 'catsequences.c` and recompile the tool.

This line you want to change is:

#define MAXLEN 1000000

Although this means that the total length of all the seqeunces you are trying to concatentate is greater than 1 million bp. Please make sure that this is as expected before changing the code.

I need a different delimiter character in the sequence names than the default "|", "." or " " (space)

Add (or remove) characters between the " " as needed on line 16 of catsequences.c:

#define NAMEDELIMITER " |." 

Then recompile (build) the tool.