Hi everyone, I am performing the phylogenetic reconstruction of my non-model organism, I am working with the BUSCOs output (single copy sequences files) form 7 different species, I have more than 1250 small multi-fasta files generated as output by Guidance2 software.
>PAS_EOG092D4S9W MAHRIISQVVLTGARVFGRAFAEAYKQASASQ >PSE_EOG092D4S9W MAHRIVTQVLITGARVFGR >PSE_EOG092D4S9W MAHRIVTQVLVTGARVFGRAFAEAYKQASASQKFAQQN
I am trying to do my Bootstrapping but the sequence generated are not accepted by raxlm program I have to uniform them to the same length but I can not find a program to do that recursively.
This is how the multifasta should looks like. However, every single files has sequences with different lengths so I can not choice an standard number to trimming the sequences. I think that the solution could be calculate the length smaller sequence and then cutting the others using the calculated length as a reference.
>PAS_EOG092D4S9W MAHRIISQVVLTGARVFGRAFAEAYKQASAS >PSE_EOG092D4S9W MAHRIVTQVLITGARVFGRAFAEAYKQASAF >PSE_EOG092D4S9W MAHRIVTQVLVTGARVFGRAFAEAYKQASA
Can anybody help to untingling this issue me please