Concatenating single gene alignments

Question

[matejasoretic]

I have run Panaroo on 160 genomes and as one of the outputs I have received single gene alignments files for each gene in all of the genomes they are present in. I wish to concatenate several of these files in a way such that within the concatenated files, sequences which originated from the same genome are concatenated together. What is a simple way of achieving this using R or the linux terminal?

Answer 1

[Dave Carlson]

I like to use the pxcat program from the phyx tool suite for MSA concatenation:

https://github.com/FePhyFoFum/phyx

You could also use PhyKit, though I haven't tried it yet:

https://jlsteenwyk.com/PhyKIT/usage/index.html#create-concatenation-matrix

Answer 2

[Mensur Dlakic]

This is what I use:

• https://github.com/nylander/catfasta2phyml