MAFFT alignments and HMM Profiles

We utlized the fasta aminoacid files (described in the section Matrices|Dataframes|FAA) of any orthogroup containing more than two CDS to compute alignments using MAFFT. These alignments can be utilized to construct gene trees for any orthogroup you may be interested in.

Utilizing the MAFFT alignments described above, we constructed Hidden Markov Model (HMM) profiles from the otrhogroups reported in our study. In our research we used the HMM profiles to quantify the abundance of interesting orthogroups across metagenomes.

The scripts describing the creation of the MAFFT alignments and the HMM profiles can be found here

Scripts to create orthogroups alignments and HMM profiles

Another useful application of these HMM profiles is to scan new genomes for specific orthogroups of interest. In the next link we provide a pipeline and a guide to annotate your genomes using the HMM databases zip file at your left.

Scripts to scan genomes using our HMM profiles