Version 2.2.0.5

Incorporate all bugs fixed.

Ancestral site concordance factor

This version implements the (unpublished) ancestral site concordance factors with two new options --ascf NUM_QUARTETS and --bscf NUM_QUARTETS. These options have not been tested with +I (invariant site) or +G (Gamma rate heterogeneity) model. So you should specify the model like -m JC or -m GTR.

Example usages:

iqtree2 -s ALN_FILE -m JC --ascf 1000
iqtree2 -s ALN_FILE -m GTR --bscf 1000

It constructs an ML tree and computes asCF or bsCF values for every internal branch by 1000 random resampling of ancestral states of 4 nodes around that internal branch.

If you want to compute asCF or bsCF on a fixed tree file, add -te TREE_FILE option.

Version 2.2.0

Introduce AliSim, an ultrafast and realistic sequence alignment simulator for phylogenetics, as an extension of IQ-Tree.
User Manual of AliSim is available at http://www.iqtree.org/doc/AliSim

- Update 1st June 2022:
Bugs fixed:

• Output long sequence names.
• Only show AliSim commands if users specify --alisim commands

- Update 25 March 2022:

• Improve indels implementation.
• Bug fixed: GC+I (continuous Gamma rate variation + invariant proportion sites)

Version 2.2.0.4

Fixed the following issues:

1. The model +I+R was printed as +I+I+R
2. The program was terminated unexpectedly when using the option -S with multiple threads

Version 2.2.0.3

1. Allow the user to set the number of digits in the .iqtree file and .treefile file by using the option "-prec [number of digits]".
2. For model mixture, allow users to set input class weight below the threshold but output a warning.

Fixed the following issues:

issue #47 -- ERROR: Alignment sequence xxx does not appear in the tree
issue #74 -- Not writing varsites.phy correctly after using ASC option

Beta version v2.2.1

This version supports the Q-Mixture model in which multiple classes have unlinked but the same type of substitution model.

For example:
MIX{GTR+FO, GTR+FO}+G (i.e. Two classes have unlinked GTR and frequencies, but share a gamma rate model and the same tree).
MIX{HKY+F, HKY+F}+G (i.e. Two classes have unlinked HKY, but share the same set of nucleotide frequencies, a gamma rate model, and the same tree).

Note that the attached binaries files are updated, but the attached source files are not. Please obtain the updated source files from the branch "model-mix".

Beta version 2.1.4-beta

Bugfixes:

• Fix crash with -bnni and non-reversible models (thanks Nancy George)

Version 2.1.3

New features:

• Compute rootstrap supports output to .rootstrap.nex file when using nonreversible models with bootstrap.
• New option --rootstrap to compute rootstrap values on a user-defined tree (-t) from a set of (bootstrap) trees. Works with unrooted trees by providing outgroup (-o option).
• New option --root-test to perform topology tests on rooting positions across all branches.
• Include series of new Q matrices from QMaker paper into ModelFinder by default.
• Update the latest LSD2 (commit 4a354eb).
• Print site of output alignment in the original order when partitioning.
• Handle -st NT2AA for partitioned models properly.

Bugfixes:

• Handling of --tree-fix option.

Version 2.1.2

Integrate the latest LSD2 version 1.9.7

Version 2.1.1

New features:

• Update latest lsd2 code by Hien
• New option --all-checkpoint to print checkpoints to 1.ckp.gz, 2.ckp.gz, etc (requested by Nick Goldman)

Bugfixes:

• Wrong complaint about NA:y date range (reported by Matt K)