Gentrius is a deterministic algorithm to generate trees from unrooted incomplete subtrees. It phylogenetics it can be applied to trees inferred with common methods such as supermatrix and supertrees to generate a set of all trees that have the same induced subtrees as an inferred tree. This set is called a stand. Stands are extremely valuable, since under many scoring functions all trees from the same stand have identical analytical score. Read more in our manuscript.
Preprint is available from bioRxiv
- O. Chernomor, C. Elgert, A. von Haeseler (2023) Identifying equally scoring trees in phylogenomics with incomplete data using Gentrius
There are several ways and inputs one can use to start the analysis. Here are the examples of command lines:
-
iqtree2 -gentrius <file 1> -pr_ab_matrix <file 2>
-
iqtree2 -gentrius <file 1> -s <file 3> -p <file 4>
-
iqtree2 -gentrius <file 5>
-
File 1: a phylogenetic tree to be analysed
-
File 2: a species per locus presence-absence matrix. First line is a number of species and the number of loci. Other lines contain species name followed by 0's and 1's (with space separator) to indicate presence/absence of gene sequences for corresponding loci.
Example: --------------- 5 3 species_1 0 1 1 species_2 1 0 1 species_3 1 1 1 species_4 1 1 0 species_5 1 1 1 -
File 3: an alignment file with concatenated loci
-
File 4: a partition info file for the alignment in file 3
-
File 5: contains a set of subtrees to be analysed
-
As the underlying problems are computationally hard, we use three different rules to stop the analysis. The thresholds can be changed by the corresponding options.
-
Rule 1: stop the analysis after generating NUM of trees. Default value: 1MLN trees.
-g_stop_t NUM - To change the threshold
-g_stop_t 0 - To turn off the rule -
Rule 2: stop the analysis after NUM of intermediate trees were visited. Default value: 10MLN trees.
-g_stop_i NUM - To change the threshold
-g_stop_i 0 - To turn off the rule -
Rule 3: stop the analysis after NUM hours (CPU time). Default: 168 hours (7 days).
-g_stop_h NUM - To change the threshold
-g_stop_h 0 - To turn off the rule -
To turn off all stopping rules use:
-g_non_stop
If no other option is used, the ouput is just the log file. The following information is provided about the analysis:
INFORMATION about input dataset:
Number of taxa: NUM
Number of partitions: NUM
Number of special taxa (row sum = 1): NUM
% of missing entries in pr_ab_matrix: NUM
Number of taxa on initial tree: NUM
Number of taxa to be inserted: NUM
SUMMARY:
Number of trees on stand: NUM
Number of intermediated trees visited: NUM
Number of dead ends encountered: NUM
Here are additional options to output more information:
-g_print - Write all generated trees into a file.
WARNING: There might be millions of trees! Use the next option to set the limit on the number of trees to be written into a file.
-g_print_lim NUM - Limit on the number of trees to be written to a file
NOTE: The program will continue generation, but will stop writing trees.
WARNING: Do not use summary statistics just on a fraction of trees! Due to the way the generation is performed, consecutive trees have more similar topologies. Therefore, the summary statistics for a fraction of generated trees might be misleading.
-g_print_induced - Write induced partition subtrees
-g_print_m - Write corresponding presence-absence matrix
-
Alternative approach: alternative initial trees
Due to complexity there might be cases, when Gentrius fails to generate any tree in reasonable time. In this case one can try generating trees using alternative approach: remove NUM of leaves, generate trees by re-inserting these removed leaves. This technique cannot guarantee generating all trees from the stand (i.e. trees compatible with a set of subtrees). However, by using this approach on simulated datasets it was possible to generate millions of trees for complex examples providing a lower bound on stand size.-g_rm_leaves NUM - To use alternative approach
-
Test set of trees
It is also possible to check, if some trees from a query set have identical set of subtrees as a representative tree (if they belong to the same stand).-g_query FILE - To perform check for a set of trees
If you have further questions, feedback, feature requests, and bug reports, please sign up the following Google group (if not done yet) and post a topic to the
https://groups.google.com/d/forum/iqtree
The average response time is one working day.
Preprint is available from bioRxiv
- O. Chernomor, C. Elgert, A. von Haeseler (2023) Identifying equally scoring trees in phylogenomics with incomplete data using Gentrius