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Operation Flow

There are 3 steps in operation.

  1. Calculation of site likelihood value (IQ-TREE)
  2. Performing AU test (CONSEL)
  3. Mapping AU test result into trees

Calculation of site-log likelihood (slnL) value

At first, NNI trees are generated. all.treeset is generated in this step. The first tree in this file is the ML tree. The other trees in this file are NNI trees. The NNI trees corresponding to nth bipartition of ML-tree are 2n + 2 and 2n + 3th trees (n starts from 0).

Second, slnL values of ML-tree are calculated. IQ-TREE is required in this step.

The command executing IQ-TREE is described below.

iqtree2 -s <sequence> -m <model> -te <ML-Tree> -z <Trees> -wsl

If file trees.sitelh exists, those steps are skipped.

Performing AU test

This process are composed by 3 steps.

  1. Generating replicates by RELL-bootstrap (makermt)
  2. Performing AU test (consel)
  3. Summarizing AU test (catpv)

These steps depends on the CONSEL package.

Generating RELL-bootstrap replicates

Replicates are generated on each treeset of bipartition. Treeset are composed by ML-tree, 1st NNI-tree and 2nd NNI-tree. If --seed option is specified, the specified value is used as seed in makermt. When seed is 0, seed is generated from system time in makermt. Seeds are generated on each makermt invokation. When seed is -1, random value is used as seed. Each bipartition has the same seed value in this case. Otherwise, the specified value works as seed. If -b, --bootstrap is specified, the number of replicates by RELL-bootstrap is changed. The value must be larger or equal to 1,000. 100,000 (default value) is recommended for it. "makermt" is required in this step. The command executing makermt is described below.

makermt --puzzle X.sitelh -s <seed> -b <the number of replicates / 10000> > X-makermt.log

If file X.rmt exists, thie step of Xth bipartition is skipped.

Performing AU test

AU test is performed for each treeset of bipartition. "consel" is required in this step. The command executing consel is described below.

consel X > X-consel.log

If file X.pv exists, this step of Xth bipartition is skipped.

Summarizing AU test

The result of AU test is summarized for each treeset. "catpv` is required in this step. The command executing catpv is described below.

catpv X > X.catpv

If file X.catpv exists, this step of Xth bipartition is skipped.

Mapping AU test result into trees

The results of AU test are mapped in ML-tree. result.tree represents the mapped file. X.catpv files are used for mapping Xth bipartition. If any NNI-tree corresponding to Xth bipartition is/are not rejected by AU test, Xth bipartition is not supported by AU test. If all NNI-trees corresponding to Xth bipartition are rejected, Xth bipartition is supported by AU test.

After the mapping, temporary files are deleted. If --output-tmp-files option is specified, temporary files are archived at tmp-output.tar.gz file.

Multi-threading

-T, --thread option is useful for multi-threading operation.

In site likelihood value calculation, the specified value is used as -T option of IQ-TREE. In execution of CONSEL, CONSEL processes (makermt, consel, catpv) runs parallely (CONSEL doesn't supports multi-threading operation).