The sequence selection process for a single alignment file is summarized on a flowchart (Fig. 1) and described below.
Others, i.e. Dali (Holm and Sander, 2000) and Matras (Kawabata and Nishikawa, 2000), whose results are among the ones in the highest agreement with the standard protein databases, allow distance distortions not controlled by a single transformation although the score for a single alignment pair depends on all others pairs.
eNumber of consensus sequences for which a single alignment fits the above criteria.
In the second step, the pileup model is first used to infer variants for single alignment column followed by phasing model, where the already inferred variants would not be considered.
For ribosomal proteins, 48 individual alignments were concatenated into a single alignment for analysis.
For each TFR we identified the single alignment net that contained the greatest number of alignable TFR bases, this ensured that each TFR could be mapped to no more than one loci in the second genome.
The short-read aligner Bowtie version 0.12.7 [ 42] was used for read mapping, using default mismatch parameters, and allowing only a single alignment for each read.
Hapler's added robustness does come at a computational cost, but experimental runtime analysis indicates that runtime will nevertheless be adequate for single alignments up to 100 kilobases in length, though low levels of phasing information are likely to prevent useful results over regions of this size.
These models vary in complexity, ranging from the treatment of insertion and deletion events (indels) as single-nucleotide events [ 13] to the modeling of complex length distributions for indels [ 9, 14, 15], but all allow for evolutionary inference without assuming a single alignment.
The 1,197 protein sequence alignments were concatenated into a single alignment for phylogenetic inference.
