The reads are aligned to both genomes, and the best alignment for each read is retained.
We built alignment for each orthologous group using both global sequence aligner MAFFT and local sequence aligner BLASTP.
Clean reads were then aligned to the reference genome and no more than three mismatches were allowed in the alignment for each read.
Friend recalls that when he first learned yoga, every point of alignment for each posture had to be memorized separately.
Phase 2 aims to provide a nucleotidic alignment for each SCPCH retained up to this point.
FastBLAST starts with members of known families and with a multiple sequence alignment for each family.
The resulting protein sequence alignment for each gene was used in the main phylogenetic analysis as described below.
This was followed by a step of chaining and netting to produce a single-coverage alignment for each 2× assembly.
We generated the corresponding multiple sequence alignment for each set of orthologues with more than 15 sequences using MUSCLE [27].
The latest versions of 8 different multiple alignment programs (see below) were used to construct an alignment for each of the benchmark test sets.
Irrespective of evidence for positive selection, in the multiple alignment for each cluster, individual residues at each position were examined for polymorphism that correlated to tissue-specificity.
