POInT (Polyploidy Orthology Inference Tool; alpha) Documentation

Revision History:

28-07-2020: New version of POInT correcting an error in the computation of transition probabilities for octoploidies. Analyses of octoploidies with the prior version will be incorrect.

Downloading POInT

The current release of POInT is avaliable from:

Installation:

    See the INSTALL file included with POInT for installation instructions. Note that use of the parallel OpenMP version is highly recommended for large datasets.

Dependancies:

POInT uses the lapack numerical linear algebra routines to compute transition probability matrices. The POInT distribution includes a copy of the necessary routines and the f2c package that links them to c and c++ executables. However, the configure.pl script will first search your system for installed copies of these libraries and use them in preference to the included copies if they exist. See the INSTALL document for details.

The illustration capabilities of POInT depend on the GNU plotutils package. If you want to compile POInT with this capability, first install plotutils and use ./configure.pl -p:[PATH TO libplot] when configuring POInT compilation.

Citing POInT:

Conant, G. C. and K. H. Wolfe. (2008) Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast, Genetics 179: 1681-1692.

Emery, M., M. M. S. Willis, Y. Hao, K. Barry, K. Oakgrove, Y. Peng, J. Schmutz, E. Lyons, J. C. Pires, P. P. Edger, and G. C. Conant. 2018. Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization. PLoS Genetics 14: e1007267.



Running POInT:

A basic POInT run requires a minimum of three types of files and a specification of the polyploidy type: Additionally, it is very useful to specify an assumed phylogenetic topology: if no tree file is given, POInT will try to search all possible topologies, which will be intractable for datasets larger than 5 or 6 genomes.

An example POInT analysis

Our website hosts examples for each type of file. For instance, one possible run can be done with:
% wget http://conantlab.org/data/POInT_datasets/Grass_rho/Brachypodium_distachyon_POInT_geneorders.txt
% wget http://conantlab.org/data/POInT_datasets/Grass_rho/Oropetium_thomaeum_POInT_geneorders.txt
% wget http://conantlab.org/data/POInT_datasets/Grass_rho/Setaria_italica_POInT_geneorders.txt
% wget http://conantlab.org/data/POInT_datasets/Grass_rho/Sorghum_bicolor_POInT_geneorders.txt
% wget http://conantlab.org/data/POInT_datasets/Grass_rho/Grass_rho_OptOrder.txt
% wget http://conantlab.org/data/POInT_datasets/Models/WGD_bias_fix_model.txt
% POInT -d:2 -g:Brachypodium_distachyon_POInT_geneorders.txt -g:Oropetium_thomaeum_POInT_geneorders.txt -g:Setaria_italica_POInT_geneorders.txt -g:Sorghum_bicolor_POInT_geneorders.txt -o:Grass_rho_OptOrder.txt  -m:WGD_bias_fix_model.txt 


This command will perform a global search for the optimal topology among these 4 genomes and save that topology as searchWGXexhaust_Grass_rho_OptOrder.txt0.tre.

POInT options are:


 

Option

 

Description

Example

Default

-d: Duplication/Polyploidy level -d:2 None/Required
-g: Extant genome file <-g:Brachypodium_distachyon_POInT_geneorders.txt None/Required
-o: File of double-conserved synteny blocks in ancestral order -o:Grass_rho_OptOrder.txt None/Required
-m: Model file -m:WGD_bias_fix_model.txt None/Required
-t: Assumed phylogenetic topology, Nexis format -t:Grass_rho_OptTopo.tre None/Optional
-r: Seperate root-branch model file -r:WGD_root_model.txt None/Optional
-p: File to save orthology predictions/posterior probabilities to -p:Grass_rho_OptTopo_WGD_bias_fix_post_probs.txt Optional
-c: File to save model state conditional probabilities to -p:Grass_rho_OptTopo_WGD_bias_fix_cond_probs.txt Optional
-noopt Do not perform likelihood optimization -noopt Optional
-i:# Draw tracking diagrams with # pillars per diagram (requires installation with Gnu PlotUtils, see INSTALL) -i:50 Optional
-zerolengthfixed Treat all zero length branches in the phylogeny as fixed at length=0 -zerolengthfixed Optional
-x:# Number of topologies to save from exhaustive tree searching (ignored if a topology is given) -s:2 -s:1/Optional

Notes and Tips:


Coming soon.