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endixk merged 4 commits into from
Mar 12, 2026
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Added tree inference with 3Di MSA or AA+3Di MSA #11

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2ab0533
Add option for choosing aa/3di/aa+3di MSA. Also generates partition f…
pskvins Mar 11, 2026
5426a79
Phylogenetic tree inference with 3Di / AA+3Di MSA and 3Di rate matrix…
pskvins Mar 12, 2026
00fd363
Updated README, added a new option for choosing 3Di rate matrix
pskvins Mar 12, 2026
a056ab4
Updated README
pskvins Mar 12, 2026
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22 changes: 22 additions & 0 deletions README.md
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Expand Up @@ -211,6 +211,28 @@ awk -F"\t" 'NR==FNR {a[$1];next} ($3 in a) {print $1}' /path/to/original/gene/na
unicore gene-tree --realign --threshold 30 --name /path/to/hashed/gene/names tree
```

## Phylogenetic inference with 3Di MSA
If you want to infer the phylogenetic tree with the 3Di MSA or amino acid and 3Di MSA combined (partitioned), you can use `--msa-for-tree` option in the `tree` module to specify the MSA type for tree inference.

When `--msa-for-tree 1` or `--msa-for-tree 2` is specified, the module will build the concatenated MSA with 3Di or combined (amino acid and 3Di) MSA, respectively, and run the phylogenetic inference with the concatenated MSA.

When you use the 3Di or combined MSA for tree inference, you have to make sure you provide a right path to the nexus format file containing the 3Di rate matrices. You can provide it with an option `--rate-matrix-3di`.

Example command:
```
unicore tree db/proteome_db -t iqtree --msa-for-tree 1 --rate-matrix-3di rate_matrices/matrices.nex result tree
```

You can also specify which 3Di rate matrix to use by providing the name of the matrix with `--rate-matrix-3di-name` option. If you are using IQ-TREE, this should be the name of the rate matrix defined in the nexus file. If you are using RAxML, this should be the path to the rate matrix file in PAML format.

Example command:
```
unicore tree db/proteome_db -t iqtree --msa-for-tree 1 --rate-matrix-3di rate_matrices/matrices.nex --rate-matrix-3di-name GH_LLM_3DI result tree
```

If you are using `GH_AF_3DI` or `GH_LLM_3Di` matrix, please cite:
> Garg, Sriram G., and Georg KA Hochberg. "A general substitution matrix for structural phylogenetics." Molecular Biology and Evolution 42.6 (2025): msaf124. [doi.org/10.1093/molbev/msaf124](https://academic.oup.com/mbe/article/42/6/msaf124/8157654)

## Phylogenetic inference with partition model
After running the `tree` module, you can modify the RAxML-style partition file named `combined.fasta.partitions` to run the phylogenetic inference with partition model.

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26 changes: 26 additions & 0 deletions rate_matrices/FOLDSEEK_3DI.nexus
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#nexus
begin models;
model 3DI =
0.011992313
0.008437599 0.053509031
0.069554168 0.018636955 0.010684044
0.017044607 0.018636955 0.0215826 0.050022332
0.069554168 0.013112664 0.010684044 0.07109646 0.043632459
0.098856949 0.001590694 0.001296079 0.035194913 0.001843543 0.017864982
0.024225404 0.076052086 0.010684044 0.143620377 0.007522972 0.012569516 0.002813795
0.024225404 0.037648099 0.0215826 0.143620377 0.007522972 0.017864982 0.008078758 0.119514031
0.004176869 0.00922586 0.00184211 0.035194913 0.00045177 0.006222293 0.000485146 0.0416262 0.01108926
0.017044607 0.006491168 0.007517123 0.024762578 0.043632459 0.10361504 0.002813795 0.003552863 0.005489521 0.000645798
0.017044607 0.001119187 0.000317611 0.017422554 0.000317858 0.00884371 0.000980032 0.003552863 0.003862339 0.005323544 0.001269667
0.001454785 0.004567082 0.0009119 0.017422554 0.00022364 0.001524805 8.36473E-05 0.029287528 0.005489521 0.361750658 0.000218912 0.001785052
0.140504827 0.004567082 0.003721205 0.101049 0.005293043 0.10361504 0.016319718 0.014498218 0.015761103 0.005323544 0.021142791 0.042248118 0.00063478
0.034431431 0.0264886 0.0215826 0.143620377 0.0306991 0.0512926 0.003999231 0.020606237 0.031838654 0.00374556 0.030050131 0.003605945 0.00063478 0.013670216
0.004176869 0.053509031 0.061966346 0.024762578 0.0306991 0.012569516 0.000980032 0.014498218 0.015761103 0.001304562 0.01487573 0.000216544 0.000446621 0.001658331 0.038802615
0.008437599 0.0264886 0.005288927 0.050022332 0.001843543 0.00884371 0.000980032 0.169864622 0.031838654 0.254521976 0.002564827 0.005125109 0.04313521 0.009618146 0.019208476 0.007408411
0.0489372 0.003213326 0.001296079 0.050022332 0.002620218 0.025391399 0.003999231 0.010200715 0.007802226 0.005323544 0.003645374 0.172402491 0.001822534 0.112688512 0.019208476 0.001277335 0.003470942
0.024225404 0.00922586 0.003721205 0.050022332 0.001297087 0.00884371 0.011482293 0.020606237 0.129924444 0.001854166 0.002564827 0.001785052 0.00063478 0.006767173 0.013514777 0.002580316 0.003470942 0.003763817
0.00593656 0.018636955 0.0215826 0.035194913 0.043632459 0.036088653 0.000341341 0.005049664 0.007802226 0.000454373 0.0607036 0.000152357 5.41795E-05 0.002356976 0.0783843 0.0610702 0.000850572 0.000922343 0.00061789

0.0489587 0.026488295 0.021582352 0.101047724 0.030698759 0.05129205 0.032966606 0.041625681 0.045251559 0.030875576 0.060702918 0.029724702 0.015023598 0.027614576 0.078383431 0.061069471 0.02013084 0.031026099 0.029541311 0.215995723;

end;
27 changes: 27 additions & 0 deletions rate_matrices/GH_AF_3DI.nexus
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#nexus
begin models;
model GH3DIAF =

0.206045
0.099742 5.400736
1.457346 0.436088 0.128820
0.080698 0.720726 2.116457 0.254751
6.112871 0.628550 0.785210 0.438587 3.269893
6.315523 0.126222 0.005220 0.400088 0.000100 2.247661
0.502964 6.966101 0.053012 0.772862 0.041468 0.131136 0.211629
1.053123 4.588735 4.956251 1.517048 0.099350 0.264919 0.822337 6.003063
0.015142 0.047967 0.004065 0.042708 0.000100 0.012162 0.003143 0.107788 0.039183
0.022323 0.245392 0.887613 0.023929 3.341014 7.242103 0.000100 0.010369 0.019796 0.000100
0.061828 2.101791 0.000100 0.038302 0.000100 0.018519 1.060336 0.000100 0.000100 0.008930 0.000100
0.000615 0.004749 0.000100 0.035820 0.000100 0.000100 0.000100 0.483191 0.040695 10.253329 2.766935 0.022626
6.309383 0.121769 0.078908 0.628010 0.007888 5.346546 0.786018 0.359712 0.340878 0.018811 0.046545 1.261582 0.272626
0.315525 1.031825 1.705683 2.597926 1.657803 1.217182 0.023281 0.157070 0.430942 0.019856 0.613644 0.001549 0.000100 0.276664
0.012345 5.992759 8.823413 0.024534 1.923030 0.349607 0.002102 0.012076 0.000100 0.000100 0.574042 0.000100 0.000100 0.007107 0.449860
0.112710 0.816173 0.018331 0.164966 0.004373 0.039618 0.058434 7.546948 0.254380 9.035512 0.000100 0.003265 2.120022 0.134079 0.059112 0.006286
0.393212 0.000100 0.007109 0.099923 0.002882 0.042536 0.026840 0.074493 0.037627 0.013724 0.005050 8.642995 0.004241 7.119415 0.030238 0.003855 0.028735
1.243085 0.695155 0.308668 0.850697 0.000100 0.140824 1.623621 0.870587 8.785918 0.014752 0.000100 0.000100 0.295570 7.288365 0.014823 0.000100 0.309913 1.376590
0.019982 0.530197 1.622344 0.115724 2.691451 0.767944 0.000100 0.004101 0.020893 0.000100 1.458258 0.000100 0.000100 0.017032 1.828515 1.431409 0.008965 0.000100 0.277948
0.033931 0.029677 0.022718 0.217063 0.024418 0.042391 0.009530 0.030112 0.027921 0.035267 0.054280 0.015301 0.006238 0.022522 0.106582 0.054584 0.025223 0.029034 0.008336 0.204872;

end;
26 changes: 26 additions & 0 deletions rate_matrices/GH_LLM_3DI.nexus
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#nexus
begin models;
model GH3DILLM =

0.231961
0.146826 5.090886
1.388719 0.532458 0.190308
0.110858 0.716943 2.125318 0.313970
6.388705 0.813365 0.828167 0.478477 3.327515
5.951036 0.080207 0.006321 0.335158 0.002561 2.778985
0.607573 6.904352 0.085029 0.875117 0.058443 0.193906 0.214237
1.113791 4.583128 5.234948 1.489843 0.125244 0.337944 0.822784 5.979297
0.009901 0.163928 0.009731 0.095737 0.000100 0.040187 0.001333 0.527276 0.038698
0.185462 0.241867 1.179789 0.053042 3.847074 7.247152 0.000100 0.015759 0.036690 0.000100
0.132103 2.588205 0.000100 0.118692 0.000100 0.080207 1.244845 0.018311 0.000100 0.012998 0.000100
0.000100 0.042084 0.000100 0.112098 0.000100 0.000100 0.004575 0.599114 0.044284 10.092991 3.275657 0.019718
6.179672 0.150465 0.069198 0.539983 0.009550 5.264532 0.769307 0.361928 0.414869 0.026380 0.092123 1.427081 0.417866
0.279075 1.258665 1.808066 1.860684 1.165969 1.082343 0.020568 0.179115 0.504681 0.015790 0.525574 0.009107 0.000100 0.186118
0.027139 6.152354 8.958557 0.063226 2.297381 0.389469 0.000326 0.086986 0.060145 0.000327 0.894820 0.000100 0.000100 0.006553 0.392745
0.113570 1.079416 0.029239 0.233041 0.001100 0.104413 0.076617 7.329984 0.338976 9.020506 0.000100 0.011688 2.219036 0.145406 0.087298 0.005651
0.769457 0.000100 0.017725 0.183073 0.001436 0.208658 0.035521 0.091606 0.049878 0.014484 0.000100 8.451390 0.000100 6.954269 0.043893 0.001126 0.034279
1.254860 0.794688 0.454326 0.673482 0.000100 0.227978 1.482768 0.873264 8.508743 0.024688 0.001574 0.000100 0.360825 7.563736 0.020832 0.003544 0.346383 1.696874
0.002510 0.412164 1.486427 0.162290 2.587540 0.648155 0.000100 0.001325 0.039870 0.000100 1.447960 0.000100 0.000100 0.000100 1.243411 1.340558 0.002979 0.002943 0.277948
0.021206 0.020366 0.016410 0.256866 0.024776 0.029869 0.005103 0.022589 0.019469 0.030696 0.037815 0.013012 0.005616 0.015834 0.120296 0.040434 0.017760 0.025094 0.003983 0.272807;

end;
72 changes: 72 additions & 0 deletions rate_matrices/matrices.nex
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#NEXUS
Begin models;

Model GH_LLM_3DI =
0.231961
0.146826 5.090886
1.388719 0.532458 0.190308
0.110858 0.716943 2.125318 0.313970
6.388705 0.813365 0.828167 0.478477 3.327515
5.951036 0.080207 0.006321 0.335158 0.002561 2.778985
0.607573 6.904352 0.085029 0.875117 0.058443 0.193906 0.214237
1.113791 4.583128 5.234948 1.489843 0.125244 0.337944 0.822784 5.979297
0.009901 0.163928 0.009731 0.095737 0.000100 0.040187 0.001333 0.527276 0.038698
0.185462 0.241867 1.179789 0.053042 3.847074 7.247152 0.000100 0.015759 0.036690 0.000100
0.132103 2.588205 0.000100 0.118692 0.000100 0.080207 1.244845 0.018311 0.000100 0.012998 0.000100
0.000100 0.042084 0.000100 0.112098 0.000100 0.000100 0.004575 0.599114 0.044284 10.092991 3.275657 0.019718
6.179672 0.150465 0.069198 0.539983 0.009550 5.264532 0.769307 0.361928 0.414869 0.026380 0.092123 1.427081 0.417866
0.279075 1.258665 1.808066 1.860684 1.165969 1.082343 0.020568 0.179115 0.504681 0.015790 0.525574 0.009107 0.000100 0.186118
0.027139 6.152354 8.958557 0.063226 2.297381 0.389469 0.000326 0.086986 0.060145 0.000327 0.894820 0.000100 0.000100 0.006553 0.392745
0.113570 1.079416 0.029239 0.233041 0.001100 0.104413 0.076617 7.329984 0.338976 9.020506 0.000100 0.011688 2.219036 0.145406 0.087298 0.005651
0.769457 0.000100 0.017725 0.183073 0.001436 0.208658 0.035521 0.091606 0.049878 0.014484 0.000100 8.451390 0.000100 6.954269 0.043893 0.001126 0.034279
1.254860 0.794688 0.454326 0.673482 0.000100 0.227978 1.482768 0.873264 8.508743 0.024688 0.001574 0.000100 0.360825 7.563736 0.020832 0.003544 0.346383 1.696874
0.002510 0.412164 1.486427 0.162290 2.587540 0.648155 0.000100 0.001325 0.039870 0.000100 1.447960 0.000100 0.000100 0.000100 1.243411 1.340558 0.002979 0.002943 0.277948
0.021206 0.020366 0.016410 0.256866 0.024776 0.029869 0.005103 0.022589 0.019469 0.030696 0.037815 0.013012 0.005616 0.015834 0.120296 0.040434 0.017760 0.025094 0.003983 0.272807;


Model GH_AF_3DI =
0.206045
0.099742 5.400736
1.457346 0.436088 0.128820
0.080698 0.720726 2.116457 0.254751
6.112871 0.628550 0.785210 0.438587 3.269893
6.315523 0.126222 0.005220 0.400088 0.000100 2.247661
0.502964 6.966101 0.053012 0.772862 0.041468 0.131136 0.211629
1.053123 4.588735 4.956251 1.517048 0.099350 0.264919 0.822337 6.003063
0.015142 0.047967 0.004065 0.042708 0.000100 0.012162 0.003143 0.107788 0.039183
0.022323 0.245392 0.887613 0.023929 3.341014 7.242103 0.000100 0.010369 0.019796 0.000100
0.061828 2.101791 0.000100 0.038302 0.000100 0.018519 1.060336 0.000100 0.000100 0.008930 0.000100
0.000615 0.004749 0.000100 0.035820 0.000100 0.000100 0.000100 0.483191 0.040695 10.253329 2.766935 0.022626
6.309383 0.121769 0.078908 0.628010 0.007888 5.346546 0.786018 0.359712 0.340878 0.018811 0.046545 1.261582 0.272626
0.315525 1.031825 1.705683 2.597926 1.657803 1.217182 0.023281 0.157070 0.430942 0.019856 0.613644 0.001549 0.000100 0.276664
0.012345 5.992759 8.823413 0.024534 1.923030 0.349607 0.002102 0.012076 0.000100 0.000100 0.574042 0.000100 0.000100 0.007107 0.449860
0.112710 0.816173 0.018331 0.164966 0.004373 0.039618 0.058434 7.546948 0.254380 9.035512 0.000100 0.003265 2.120022 0.134079 0.059112 0.006286
0.393212 0.000100 0.007109 0.099923 0.002882 0.042536 0.026840 0.074493 0.037627 0.013724 0.005050 8.642995 0.004241 7.119415 0.030238 0.003855 0.028735
1.243085 0.695155 0.308668 0.850697 0.000100 0.140824 1.623621 0.870587 8.785918 0.014752 0.000100 0.000100 0.295570 7.288365 0.014823 0.000100 0.309913 1.376590
0.019982 0.530197 1.622344 0.115724 2.691451 0.767944 0.000100 0.004101 0.020893 0.000100 1.458258 0.000100 0.000100 0.017032 1.828515 1.431409 0.008965 0.000100 0.277948
0.033931 0.029677 0.022718 0.217063 0.024418 0.042391 0.009530 0.030112 0.027921 0.035267 0.054280 0.015301 0.006238 0.022522 0.106582 0.054584 0.025223 0.029034 0.008336 0.204872;

Model FOLDSEEK_3DI =
0.011992313
0.008437599 0.053509031
0.069554168 0.018636955 0.010684044
0.017044607 0.018636955 0.0215826 0.050022332
0.069554168 0.013112664 0.010684044 0.07109646 0.043632459
0.098856949 0.001590694 0.001296079 0.035194913 0.001843543 0.017864982
0.024225404 0.076052086 0.010684044 0.143620377 0.007522972 0.012569516 0.002813795
0.024225404 0.037648099 0.0215826 0.143620377 0.007522972 0.017864982 0.008078758 0.119514031
0.004176869 0.00922586 0.00184211 0.035194913 0.00045177 0.006222293 0.000485146 0.0416262 0.01108926
0.017044607 0.006491168 0.007517123 0.024762578 0.043632459 0.10361504 0.002813795 0.003552863 0.005489521 0.000645798
0.017044607 0.001119187 0.000317611 0.017422554 0.000317858 0.00884371 0.000980032 0.003552863 0.003862339 0.005323544 0.001269667
0.001454785 0.004567082 0.0009119 0.017422554 0.00022364 0.001524805 8.36473E-05 0.029287528 0.005489521 0.361750658 0.000218912 0.001785052
0.140504827 0.004567082 0.003721205 0.101049 0.005293043 0.10361504 0.016319718 0.014498218 0.015761103 0.005323544 0.021142791 0.042248118 0.00063478
0.034431431 0.0264886 0.0215826 0.143620377 0.0306991 0.0512926 0.003999231 0.020606237 0.031838654 0.00374556 0.030050131 0.003605945 0.00063478 0.013670216
0.004176869 0.053509031 0.061966346 0.024762578 0.0306991 0.012569516 0.000980032 0.014498218 0.015761103 0.001304562 0.01487573 0.000216544 0.000446621 0.001658331 0.038802615
0.008437599 0.0264886 0.005288927 0.050022332 0.001843543 0.00884371 0.000980032 0.169864622 0.031838654 0.254521976 0.002564827 0.005125109 0.04313521 0.009618146 0.019208476 0.007408411
0.0489372 0.003213326 0.001296079 0.050022332 0.002620218 0.025391399 0.003999231 0.010200715 0.007802226 0.005323544 0.003645374 0.172402491 0.001822534 0.112688512 0.019208476 0.001277335 0.003470942
0.024225404 0.00922586 0.003721205 0.050022332 0.001297087 0.00884371 0.011482293 0.020606237 0.129924444 0.001854166 0.002564827 0.001785052 0.00063478 0.006767173 0.013514777 0.002580316 0.003470942 0.003763817
0.00593656 0.018636955 0.0215826 0.035194913 0.043632459 0.036088653 0.000341341 0.005049664 0.007802226 0.000454373 0.0607036 0.000152357 5.41795E-05 0.002356976 0.0783843 0.0610702 0.000850572 0.000922343 0.00061789

0.0489587 0.026488295 0.021582352 0.101047724 0.030698759 0.05129205 0.032966606 0.041625681 0.045251559 0.030875576 0.060702918 0.029724702 0.015023598 0.027614576 0.078383431 0.061069471 0.02013084 0.031026099 0.029541311 0.215995723;

End;
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