Input preparation for PAML analysis

Question

[christianbharathi]

Currently, I am studying the gene (molecular) evolution using PAML software. I am facing problem while preparing input file. After alignment (MSA) of all genes there is too much of gabs between nucleotide which the software does not taking as a input.

In tutorials I have seen that all sequences are same length after alignment. When I trying to edit the gene sequences to bring in to same length, coding regions are getting deleted and results is not correct.

Can anyone suggest me to prepare appropriate input file for PAML (selection and evolution analysis)?

Thanking you

Answer 1

[mbens]

Gblocks is able to remove poorly aligned regions and gaps from alignments.

Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17, 540-552.

[christianbharathi]

Thank you for the response