Words similar to concatenated
Example sentences for: concatenated
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Similar tree topologies were obtained when the ribosomal protein data were analyzed using the neighbor-joining method and when bacterial phylogeny was analyzed separately by using a concatenated alignments of 51 ribosomal proteins shared by all bacteria (data not shown).
The alignments of the 32 ribosomal proteins conserved in all bacterial and archaeal species were concatenated head-to-tail and treated as a single alignment containing 4821 columns.
Posterior probabilities of concatenated files were computed using Bayesian inference [ 32 ] (Jones model with gamma estimated from data; 10,000 generations; 4 chains with temp = 0.2).
Pairwise evolutionary distances between the sequences in concatenated alignments were calculated using the Dayhoff PAM model as implemented in the PROTDIST program of the PHYLIP package [ 44 ] . A distance tree was constructed from the resulting distance matrix by using the least-square [ 46 ] method as implemented in the FITCH program of PHYLIP [ 44 ] . The maximum likelihood tree was constructed with the JTT-F model of amino acid substitutions [ 47 ] , as implemented in the ProtML program of the MOLPHY package [ 48 ] , by optimizing the least squares tree with local rearrangements.
The topologies of the resulting trees were compared to each other and to the topology of a phylogenetic tree constructed on the basis of a concatenated alignment of ribosomal proteins, which was chosen as the (hypothetical) species tree of the organisms involved [ 13].