How to concatenate two gene MSA files with same organism to make a phylogeny of both he genes as one single concatenated phylogeny?

Question

[Ap1438]

all_rbcL.fasta:

MK60111.1
sequence
NC_110014.1
sequence
NC_110454.1
sequence
KT25472.1
sequence

all_matK.fasta:

NC_110014.1
sequence
MK60111.1
sequence
NC_110454.1
sequence
KT25472.1
sequence

And I want OUTPUT to be

NC_110014.1
sequence(matk)sequence(rbcl)
KT25472.1
sequence(matk)sequence(rbcl)

i.e. vertically one after another two gene sequences

I have 2 different multiple sequence alignment files of same organisms with ID as shown above.These 2 files are of 2 genes i.e. rbcl and matk and i want to concatenate both the genes i.e. rbcl+matk to make phylogeny.

I don't know how to concatenate both files with same organisms for these 2 genes .Can anyone help me on this?

Answer 1

[Mensur Dlakic]

This perl script will do what you want. It is important that alignments have the same order and same names for sequences.

By the way, for two MSAs you can easily do it by hand by copying and pasting the sequences in the same order.

[Ap1438]

Thank you for your valuable time and suggestion. The perl script is not working in my case because i have two different MSA gene files which are of different lengths (Same organisms in both the file i.e. 45 in total ). The perl script requires files to have equal length of the sequences.

I can do it manually now because i have 2 small file with 45 sp. entries but want to do it in command line so that if required can be done in command line in less time.

[Mensur Dlakic]

The perl script requires files to have equal length of the sequences.

The script requires all sequences within the same alignment to have the same length. Which they should, because differences in length get filled in by indel symbols. Different MSA files don't need to have the same length, but they do need to have the same group of sequences, and in the same order. I don't know if you actually tried the script, but if it didn't work for you it wasn't because MSA files had different lengths.

[Ap1438]

Yaa i got it there was some error in my file. But it didn't produce the desired output.Like i have mentioned above.