Figure 4
From: OrthoSelect: a protocol for selecting orthologous groups in phylogenomics
Rebuilding the multiple sequence alignment. The figure illustrates how OrthoSelect refines the multiple sequence alignments (MSA) created so far. Based on the MSA a hidden Markov Model (HMM) is build. Additionally, all EST libraries are translated using ESTScan with different matrices (ranging from Arabidopsis thaliana to Homo sapiens). The software hmmsearch from the HMMER package then used the HMM to search all translated sequences and selecting the best hit from each taxon above a given threshold. From these hits the new MSA is then computed