Sentence examples for alignment analyses are from inspiring English sources
Multiple sequence alignment analyses are based largely on the assumptions that evolutionarily-conserved amino acids are more likely to be functionally important than nonconserved amino acids and substitutions involving chemically similar amino acids are less likely to be damaging than substitutions involving chemically different amino acids.
Multiple sequence alignment analyses were performed using ClustalX (version 1.83) program.
Multiple alignment analyses were performed using MUSCLE (version 3.6) program [ 85].
A striking result of the alignment analyses is that the H-Y-E catalytic site motif is fully conserved only in subgroups 1 and 2 (pARTs 1 6).
The GUIDANCE alignment analyses were conducted using the MAFFT algorithm and 100 bootstrap replicates, with variable amino acid position columns identified using the GUIDANCE method and then removed based on a column-score cutoff of <0.93.
DNA alignment analyses were conducted by using ClustalW version 1.83 (www.ebi.ac.uk/clustalw), and nucleotide substitutions were identified by using BioEdit version 7.0.1 (Isis Pharmaceuticals, Inc., Carlsbad, CA, USA) (7 ).
Thanks to the large amount of signal contained in genome-wide sequence alignments, phylogenomic analyses are converging towards highly supported trees.
Accession numbers of RECKs used for sequence alignment and phylogenetic analyses are as follows: Tribolium (XP_974450), Nematostella vectensis (XP_001635685), Drosophila melanogaster (NP_648733), Apis mellifera (XP_392031); Aedes aegypti (XP_001657759); Homo sapiens (NP_066934).
Nucleotide alignment and phylogenetic analyses are deposited in treeBASE under study 14243 (http://purl.org/phylo/treebase/phylows/study/TB2 S14243).
After alignment, phylogenetic analyses were conducted by using maximum-likelihood and Bayesian methods (1, 2 ).
Sequence alignment and analyses were performed online using the BLAST program available at the National Center for Biotechnology Information web page http://www.ncbi.nlm.nih.gov.nih.gov
