For the construction of reference alignments we used "seed" alignments from the Rfam database version 7.0 [ 24, 23].
This genome is then used as reference for homology searches in further organisms and for the construction of multiple alignments.
Sixteen clades from the parsimony consensus tree inferred were selected as groups for the construction of ITS alignments.
7 structural entries of odorant-binding proteins (OBPs; PDB ID: 1dqe, 2wcj, 2gte, 2erb, 3k1e, 3bfh, 1ow4), available then, were used for the construction of the structural alignment.
For each family, the reference alignment was constructed using a semi-automatic protocol similar to the one developed for the construction of the BAliBASE [50] alignment benchmark.
We used the VISTA pipeline infrastructure [ 29] with Shuffle-LAGAN glocal chaining algorithm [ 30] applied to local alignments produced by translated BLAT [ 31] for the construction of genome-wide pairwise human/mouse alignment.
We used the VISTA pipeline infrastructure47,48 for the construction of genome-wide pairwise DNA alignments between E. grandis and Populus trichocarpa.
In 1974, PA 284 was adjusted for the construction of the new U.S. Route 15 alignment.
Multiple alignments of the N-proximal regions (from the start of the conserved DBD domain to the end of the HR-A/B region) of Hsf proteins from pepper, tomato and Arabidopsis were performed by CLUSTALW and the result of alignment was used for the construction of phylogenetic tree [ 1, 41] using MEGA 5.10 [ 67].
This software uses several kinds of software for the workflow such as MUSCLE multiple alignment, Gblocks for the alignment curation, PhyML for the construction of the phylogenetic tree, and TreeDyn for the visualisation of phylogenetic tree.
