Meta [ 48] was then used to find the best meta-alignment of the orthologous promoters TF-maps (with parameters: a = 0.5, l = 0.1, m = 0.1).
A local meta-alignment is a concatenate of all alignment fragments of a fixed type (for example, coding alternative regions) for one particular gene.
A global meta-alignment is the concatenate of local meta-alignments of a fixed type for all genes of a fixed group (for example, for all fast-evolving genes).
Provided fast methods are used to generate the original alignment, the meta-alignment procedure of M-Coffee can use a sparse DP procedure that takes advantage of the strong agreement between the considered alignments.
A subset of SNP loci present among all data sets (core) were identified and used to generate a meta-alignment using an in-house Perl script for downstream analysis.
To evaluate the robustness of the estimates for evolutionary parameters of the global meta-alignments, we used bootstrapping to form 2000 alighments of the same length for reach global meta-alignment and estimated amino-acid identity, dN, dS, and ω = dN/dS.
Alignments were run in forward and reverse direction (that is, using the Head or Tail approach [ 50]), and the six resulting alignments were combined with M-COFFEE [ 51], then the resulting meta-alignment was trimmed with trimAl v1.3 [ 35], (consistency-score cutoff 0.1667, gap-score cutoff 0.1).
Global meta-alignments (concatenated alignment fragments across all considered genes and across three rate bins, see Methods) of five types (C, A, AN, AI, AC) were used.
Secondly, structural homology to previously defined protein folds in Protein Data Bank (PDB) [ 51] or Pfam [ 19, 20] were searched for using a newly improved version of the meta-predictor, Meta-BASIC [ 52], which combines sequence profile, secondary structure, and prediction of the burial states of individual amino acid with various scoring systems and meta profile alignment algorithms.
The meta-diaphyseal alignment was corrected, and two Schanz pins were inserted at the diaphysis.
