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Example sentences for: jtt

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For all three possible unrooted tree topologies maximum-likelihood values and posterior probabilities were calculated using in-house JAVA programs that were written utilizing classes from the Phylogenetic Analysis Library version 1.0 [ 54 ] and parts of Vanilla package version 1.0 [ 54 ] . If not indicated otherwise, likelihood values were estimated using the automatically selected suitable substitution model (chosen from BLOSUM62, CPREV, Dayhoff, JTT, MTREV24, VT and WAG) with no ASRV.
For the maximum-likelihood trees, the experimental versions of the programs PROML (no assumption of molecular clock) and PROMLK (molecular clock assumed) from PHYLIP version 3.6a3 were used with the JTT evolutionary model and with the assumption of constant change rate between sites.
Branch lengths and their confidence intervals were calculated with TREE-PUZZLE 5.0 [ 46 ] using the JTT or the HKY model for substitution respectively, and assuming an among site rate variation described by a gamma distribution.
Posterior probabilities were also calculated with MrBayes version 2.01 [ 31 ] . Each QuartOP was analyzed with two simultaneous Markov chains for 25,000 cycles under the JTT substitution model [ 55 ] without ASRV.
In all runs samples were taken at each cycle; two chains and the JTT substitution model [ 55 ] without ASRV were used.