Words similar to concatenated
Example sentences for: concatenated
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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].
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 sequences were concatenated in batches of 96 into a text file using FASTA format and submitted for a batch BLASTN search using the interface program BLASTCL3.
An independent phylogenetic study of concatenated ribosomal proteins has been recently published [ 32 ] . The main specific conclusion reported in this study was the apparent association of Synechocystis with Gram-positive bacteria, although instability of the tree topology dependent on the subset of sites used for analysis was noticed.
When assessed against the topology of the tentative species tree based on the concatenated alignments of ribosomal proteins [ 13], fusions showed a scattered distribution in phyletic patterns (depicted by columns in Figure 1).
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