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For each of the 13 most conserved COG groups, one maximum likelihood tree with 100 bootstrap replicates was built.
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For leopard cats, a separate Maximum-Likelihood tree based on a heuristic search and 500 bootstrap replicates, as well as a Neighbor-Joining tree with Jukes-Cantor distances and 1000 bootstrap replicates were built using PAUP* with 575 bp of cytochrome b and sequences included from the earlier study [23], using the fishing cat as outgroup.
One thousand bootstrap (BS) replicates were built under the WAG model.
The number of bootstrap replicates was 1000.
The number of bootstrap replicates was set on 1,000 replicates.
The bootstrap replicates were used to build a consensus tree applying the majority rule option (-m PROTGAMMAIJTTF -J MR).
A maximum likelihood (RAxML) tree was built and the results of 100 bootstrap replicates were used to determine branch support in an unrooted phylogeny.
The phylogeny was built with PhyML using data from all 50 genomes and 100 bootstrap replicates were run.
Ten thousand bootstrap replicates were performed.
Bootstrap replicates were performed using 1000 replicates.
Five hundred bootstrap replicates were generated.
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