Can you handle the (Linux/Mac) commandline? What you want can be most easily achieved with existing biopython modules. In fact, I already have a very simple script for producing relaxed interleaved phylip-alignment-files from aligned fastas. But it requires python 2.7+ and biopython. Also you can only use it via the unix commandline and it currently only handles aligned fastas with "-" as placeholder for gaps (so if the sequences/alignments do not have identical lengths, it will produce an error). You are free to use it, if it helps. Remember to use the "-r" argument for relaxed phylip if you do use it.

Hi everyone,

Here is a basic perl script to convert a fasta formated alignement into a relaxed phylip format. The output works well as input for partionfinder2.

This script doesn't need any requirement (except perl of course which should be installed).

It will be suitable for you if the biopython requirement of the nice John's script could not be fitted.

https://github.com/npchar/Phylogenomic/blob/master/fasta2relaxedPhylip.pl

Usage: ./fasta2relaxedPhylip.pl -f -o

-f

-o

-h Displays this help and exit

Hope it helps

Thanks a lot, Jhon and Pierre.

Hi,

I use Aliview http://ormbunkar.se/aliview/ which basically does all the formats and is a gread viewer and editor.

According to me its the best I have seen so far especially for large sequence alignments

Alex, that’s true. AlliView has a great Option for formating alignments. However, I was looking for a command line application

I've found a very good function for R. Allows rapid conversion and the relaxed Phylip files can be used directly for RAxML without any problems

https://rdrr.io/github/fmichonneau/chopper/man/fas2phy.html

Thanks Fernando Roa

with Ape in R

require(ape)

mydata=read.dna("mydata.fas", format="fasta")

write.dna(mydata, "mydata.phy", format="interleaved", nbcol=-1,colsep="")