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iqtree / iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
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Despite passing `--output-multifurcating-tree`, resulting tree is bifurcating, when run in cmaple mode #283

Open corneliusroemer opened 1 month ago

corneliusroemer commented 1 month ago

I hoped that passing --output-multifurcating-tree for cmaple mode would results in a multifurcating tree, in the way that --polytomy does for normal iqtree mode, but apparently it's not working for me.

Repro:

Get alignment:

curl -L https://github.com/user-attachments/files/16381510/repro.fasta.zst.txt -o - | zstdcat > masked-delim.fasta

Run iqtree in cmaple mode with --output-multifurcating-tree:

iqtree2 -s masked-delim.fasta -m GTR -nt AUTO --redo --pathogen-force --output-multifurcating-tree -out-mul-tree                                                            
IQ-TREE multicore version 2.3.5 for MacOS ARM 64-bit built Jul 19 2024
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt,
Dominik Schrempf, Michael Woodhams, Ly Trong Nhan, Thomas Wong

Host:    kb-kbbp01-plm98.pz.unibas.ch (SSE4.2, 32 GB RAM)
Command: iqtree2 -s results/lineage-b.1/masked-delim.fasta -m GTR -nt AUTO --redo --pathogen-force --output-multifurcating-tree -out-mul-tree
Seed:    432378 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Thu Jul 25 19:12:48 2024
Kernel:  SSE2 - auto-detect threads (10 CPU cores detected)

Reading an alignment
Running [C]MAPLE algorithm...
Performing placement
Added 1000 samples
1993 sequences have been added to the tree.
Applying a normal tree search
Processed topology for 1000 nodes.
Processed topology for 2000 nodes.
Processed topology for 3000 nodes.
Processed topology for 4000 nodes.
Optimizing branch lengths
Tree log likelihood: -299084.0817599534

MODEL: GTR

ROOT FREQUENCIES
A                       C                       G                       T
0.368031        0.157026        0.15659 0.318353

MUTATION MATRIX
        A                       C                       G                       T
A       -5328.36        179.333 4901.76 247.262
C       420.312 -13067.9        178.314 12469.2
G       11520.5 178.811 -12210.2        510.888
T       285.847 6150.41 251.294 -6687.55

Analysis results written to:
Maximum-likelihood tree:       results/lineage-b.1/masked-delim.fasta.treefile
Screen log file:               results/lineage-b.1/masked-delim.fasta.log

CMAPLE Runtime: 27.4255120754s
Date and Time: Thu Jul 25 19:13:15 2024

Inspect result: it should be multifurcating (due to large polytomy) but it is bifurcating instead.

Resulting tree is in here, as well as log: repro.zip

corneliusroemer commented 1 month ago

I've tried passing --make-consistent as well, but does not seem to have an effect either