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Concatenating single gene alignments

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?

panaroo multiple sequnce alignment msa r
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updated by Ram Ram • written by matejasoretic • matejasoretic

2 answers

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

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written by Dave Carlson Dave Carlson

This is what I use:

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written by Mensur Dlakic Mensur Dlakic

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