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Michal Motyka
Nov 1, 2017, 10:38:26 AM11/1/17
to IQ-TREE
Hi,
I am tryning to run IQtree with constrained topology for several taxa (-g constrained tree in newick formate), but the results are not constrained and the tree is the same as from unconstrained analysis. I followed tutorial: 5.5 Constrained tree search without any success. I would like to ask if could someone help me to figure this out?
version: IQ-TREE multicore version 1.5.5 for Linux 64-bit built Oct 22 2017 Copyright (c) 2011-2017
command: iqtree -s COI_Neo.phy -g constrained.tree -m JC -nt 2
part of log:
Reading alignment file COI_Neo.phy ... Phylip format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 25 sequences with 723 columns and 398 patterns (341 informative sites, 326 constant sites)
Gap/Ambiguity Composition p-value
1 ELAR047Oxy 0.00% passed 75.97%
..........
25 LAMR110 0.00% failed 1.05%
**** TOTAL 0.13% 9 sequences failed composition chi2 test (p-value<5%; df=3)
Reading constraint tree constrained.tree...
NOTE: BYRElLip is identical to BYRElLim but kept for subsequent analysis
Creating fast initial parsimony tree by random order stepwise addition...
0.003 seconds, parsimony score: 1981 (based on 341 informative sites)
Thanks for your comments in advance.
Cheers,
Michal
I am tryning to run IQtree with constrained topology for several taxa (-g constrained tree in newick formate), but the results are not constrained and the tree is the same as from unconstrained analysis. I followed tutorial: 5.5 Constrained tree search without any success. I would like to ask if could someone help me to figure this out?
version: IQ-TREE multicore version 1.5.5 for Linux 64-bit built Oct 22 2017 Copyright (c) 2011-2017
command: iqtree -s COI_Neo.phy -g constrained.tree -m JC -nt 2
part of log:
Reading alignment file COI_Neo.phy ... Phylip format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 25 sequences with 723 columns and 398 patterns (341 informative sites, 326 constant sites)
Gap/Ambiguity Composition p-value
1 ELAR047Oxy 0.00% passed 75.97%
..........
25 LAMR110 0.00% failed 1.05%
**** TOTAL 0.13% 9 sequences failed composition chi2 test (p-value<5%; df=3)
Reading constraint tree constrained.tree...
NOTE: BYRElLip is identical to BYRElLim but kept for subsequent analysis
Creating fast initial parsimony tree by random order stepwise addition...
0.003 seconds, parsimony score: 1981 (based on 341 informative sites)
Thanks for your comments in advance.
Cheers,
Michal
Bui Quang Minh
Nov 1, 2017, 2:23:13 PM11/1/17
to IQ-TREE, Michal Motyka
Hi Michal,
The command line looks OK. However, it’s hard to help here without looking at the trees. Thus can you please send the tree figures for both the input constraint tree and the resulting ML tree?
Cheers, Minh
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Bui Quang Minh
Center for Integrative Bioinformatics Vienna (CIBIV)
Campus Vienna Biocenter 5, VBC5, Ebene 1
A-1030 Vienna, Austria
Phone: ++43 1 4277 74326
Email: minh.bui (AT) univie.ac.at
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