PhyloSift is a suite of software tools to conduct phylogenetic analysis of genomes and metagenomes.
Using a reference database of protein sequences, PhyloSift can scan new sequences against that database for homologs and identify the phylogenetic relationship of the new sequence to the database sequences. During this procedure, high quality alignments of codon and amino acid sequence are generated.
PhyloSift is open source software freely available on GitHub: https://github.com/gjospin/PhyloSift
If you’re having problems with your analysis in PhyloSift, try our Google Group for user support: https://groups.google.com/d/forum/phylosift