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Output files

seq.fasta

Represents the sequences. This is the copy of sequence file specified in -s, --seq option.

best.tree

Represents the ML-tree. This is the copy of tree file specified in -t. --tree option.

result.tree

Represents the mapped ML-tree.

Bipartition format

-f, --out-format specifies the format of bipartition. Some keywords of format were replaced by specified values from tests below. You should be careful that these keywords are recognized as "case-sensitive".

  • {src}: Replaced by the evaluation value in source tree file (BP, UFBP, SH-aLRT etc.)
  • {bin}, {au-bin}: Replaced by whether the 0/1 value representing the bipartition was supported by AU test or not.
    • 1 represents the bipartition was supported (all alternative trees were rejected).
    • 0 represents the bipartition was not supported (any alternative trees were not rejected).
  • {p}, {au-p}: Replaced by the max p-value by AU test of alternative trees.
  • {sh-bin}: 0/1 value representing the bipartition was supported by SH test.
  • {sh-p}: Max p-value by SH test of alternative trees.
  • {kh-bin}: 0/1 value representing the bipartition was supported by KH test.
  • {kh-p}: Max p-value by KH test of alternative trees.
  • {wsh-bin}: 0/1 value representing the bipartition was supported by weighted SH test.
  • {wsh-p}: Max p-value by weighted SH test of alternative trees.
  • {wkh-bin}: 0/1 value representing the bipartition was supported by weighted KH test.
  • {wkh-p}: Max p-value by weighted KH test of alternative trees.
  • {dlnL}: Minimum of observed log-likelihood difference between the ML tree and alternative trees.
  • {pp}: Bayesian posterior probability (PP) of the ML tree calculated by BIC approximation.
  • {bp}: Bootstrap probability of the ML tree. This value obtained by CONSEL is multiplied by 100.
  • {mbp}: Bootstrap probability of the ML tree calculated by multiscale bootstrap. This value obtained by CONSEL is multiplied by 100.

Examples

Format Source Evaluation AU-test support Max NNIp-value Output
{src}/{bin} (Default) 100 + 1e-50 100/1
{src}/{bin} (Default) 98 - 0.07 98/0
{src}/{bin}/{p} 100 + 1e-50 100/1/1e-50
{bin}/{src} 100/0.99 + 3e-27 1/100/0.99
S{src}_A{bin}P{p} 67 - 0.51 S67_A0P0.51

summary.txt

Represents the summary of operation. This file has 4 sections.

  • Summary
  • Best tree
  • Not rejected NNI trees
  • Result tree

Summary

Represents the parameters of operation and total time of operation.

Best tree

The same as best.tree.

Not rejected NNI trees

List of the NNI trees which are not rejected by AU-test. This section is formatted as TSV.

1st column represents the p-value of tree. 2nd column represents the NNI-tree.

Result tree

The same as result.tree.

indexed.tree

Represents the tree mapped by bipartition index. Each index represents the operation number.

tmp-output.tar.gz

This file has all temporary files. This file is generated when --output-tmp-files option is specified.

File list

Name Generated by Description
all.treeset AUTOEB Represents the NNI tree
trees.ckp.gz IQ-TREE Generated in calculating site likelihood values of trees
trees.iqtree
trees.log
trees.sitelh
trees.treefile
X.sitelh AUTOEB Represents site lilelihood values of ML tree and two NNI trees about a bipartition
X.rmt CONSEL (makermt) Generated in RELL-boostrap
X.vt
X-makermt.log AUTOEB Generated in redirecting of output by makermt
X.ci CONSEL (consel) Generated in AU-test
X-pv
X-consel.log AUTOEB Generated in redirecting of output by consel
X.catpv AUTOEB Generated in redirecting of output by catpv