An add-on to the phylogenetic Ranger-DTL framework that identifies likely Horizontal Gene Transfers (HGTs) to create a maximal consistent set of relative timing constraints.
Summary: Identifies transfers > Processes transfers > Removes contradictions > Creates constraints
Before starting you will have to download the Ranger-DTL software.
To use SummarizeOptTransfers the following prerequisites will need to be installed:
-
Python 2.7 or later and Python 3.6 or later
-
python 2 scipy module
$ pip2 install scipy
- python 3 six module
$ pip3 install six
- python 3 numpy module
$ pip3 install numpy
- python 3 ete3 module
$ pip3 install ete3
Description: Python 3 script that uses SummarizeOptRootings_recipient.py, SummarizeTransfers.py, MaxTiC.py, and SummarizeMaxTiC.py to take a species tree and a directory of gene trees as input to return a directory of output data containing files with all of the most likely transfers (HGTs) and relative constraints along with their support values determined from the gene trees.
All input trees must be fully binary and expressed using the Newick format terminated by a semicolon.
The species tree must be rooted and species names in each tree must be unique. Note: Internal nodes must not be labeled.
ex. ((speciesA, speciesB), speciesC);
Each leaf in each gene tree must be labeled with the name of the species from which that gene was sampled.
ex. (((speciesA, speciesC), speciesB), speciesC);
Input: Species tree with unlabeled internal nodes, Directory of gene trees
$ python3 SummarizeOptTransfers_gene.py species_tree gene_tree_dir
Output: Directory of the following form:
|-- SummarizeOptTransfers_gene_output
|-- MaxTiC_out
|-- MaxTiC_conflicting
|-- MaxTiC_consistent
|-- MaxTiC_console_output
|-- MaxTiC_informative
|-- SummarizeOptRootings_out
|-- long0001
|-- ...
|-- long9999
|-- SummarizeTransfers_out
|-- SummarizeTransfers_output
|-- SummarizeTransfers_output_constraints
|-- maximal_consistent_set_constraints
|-- species_tree_label
Optional parameters:
-h, --help show this help message and exit
-o OUTPUT_DIR specify output name (default:
SummarizeOptTransfers_gene_output)
-D DUPLICATION_EVENT_COST
specify a list of comma delimited duplication event
costs (integers) (default: 2)
-T TRANSFER_EVENT_COST
specify a list of comma delimited transfer event costs
(integers) (default: 3)
-L LOSS_EVENT_COST specify a list of comma delimited loss event costs
(integers) (default: 1)
-n SAMPLE_VALUE set the number of sampled optimal reconciliations for
each rooting (default: 100)
--seed SEED_VALUE set the seed value (integer) used in Ranger-DTL, if
false then random integer is chosen (default: False)
--dated use dated version of Ranger-DTL (default: False)
-t TRANSFER_CONFIDENCE_PERCENTAGE
specify a transfer confidence percentage value
(default: 100)
-m MAPPING_CONFIDENCE_PERCENTAGE
specify a mapping confidence percentage value
(default: 100)
-r RECIPIENT_CONFIDENCE_PERCENTAGE
specify a recipient confidence percentage value
(default: 100)
-c CUTOFF_VALUE specify a cutoff value to filter out transfers with
less confidence than cutoff (default: 1)
--internal show internal nodes only (default: False)
--short shorten runtime by not running MaxTiC or
SummarizeMaxTiC (default: False)
-s LOCAL_SEARCH_TIME specify a local search time (in seconds) to improve
MaxTiC results (default: 180)
--quiet suppress process output (default: False)
--version show program's version number and exit
Description: Python 3 script that uses SummarizeTransfers.py, MaxTiC.py, and SummarizeMaxTiC.py to take a species tree and a directory of long files (output from SummarizeOptRootings_recipient.py) as input to return a directory of output data containing files with all of the most likely transfers (HGTs) and relative constraints along with their support values determined from the gene trees. Note: This version of SummarizeOptTransfers has a much shorter runtime due to absence of calling Ranger-DTL many times.
All input trees must be fully binary and expressed using the Newick format terminated by a semicolon.
The species tree must be rooted and species names in each tree must be unique. Note: Internal nodes must be labeled using the same nomenclature as the long files.
ex. ((speciesA, speciesB)n2, speciesC)n1;
Input: Species tree with labeled internal nodes, Directory of long files (output from SummarizeOptRootings_recipient.py)
$ python3 SummarizeOptTransfers_long.py species_tree long_dir
Output: Directory of output files of the following form:
|-- SummarizeOptTransfers_long_output
|-- MaxTiC_out
|-- MaxTiC_conflicting
|-- MaxTiC_consistent
|-- MaxTiC_console_output
|-- MaxTiC_informative
|-- SummarizeTransfers_out
|-- SummarizeTransfers_output
|-- SummarizeTransfers_output_constraints
|-- maximal_consistent_set_constraints
|-- species_tree_label
Optional parameters:
-h, --help show this help message and exit
-o OUTPUT_DIR specify output name (default:
SummarizeOptTransfers_long_output)
-t TRANSFER_CONFIDENCE_PERCENTAGE
specify a transfer confidence percentage value
(default: 100)
-m MAPPING_CONFIDENCE_PERCENTAGE
specify a mapping confidence percentage value
(default: 100)
-r RECIPIENT_CONFIDENCE_PERCENTAGE
specify a recipient confidence percentage value
(default: 100)
-c CUTOFF_VALUE specify a cutoff value to filter out transfers with
less confidence than cutoff (default: 1)
--internal show internal nodes only (default: False)
--short shorten runtime by not running MaxTiC or
SummarizeMaxTiC (default: False)
-s LOCAL_SEARCH_TIME specify a local search time (in seconds) to improve
MaxTiC results (default: 180)
--quiet suppress process output (default: False)
--version show program's version number and exit
Description: Python 3 script that aggregates reconciliations across all optimal rootings of gene trees. Slightly modified SummarizeOptRootings.py script that has the same input/output with the option to supply a multiple event cost sets. See documentation in the Ranger-DTL manual.
Description: Python 3 script that takes a species tree and a directory of long files as input to return a file of the most likely transfers (HGTs) with support values and file names. Also a file of constraints is generated from the transfers to be used as input for MaxTiC.py. This program parses all of the input long files to extract the transfer data. After normalizing and filtering the data it is written to output files for further use.
All input trees must be fully binary and expressed using the Newick format terminated by a semicolon.
The species tree must be rooted and species names in each tree must be unique. Note: Internal nodes must be labeled using the same nomenclature as the long files.
ex. ((speciesA, speciesB)n2, speciesC)n1;
Input: Species tree with labeled internal nodes, Directory of long files (output from SummarizeOptRootings_recipient.py)
$ python3 SummarizeTransfers.py species_tree long_dir
Output: File containing transfers, File containing constraints
|-- SummarizeTransfers_output
|-- SummarizeTransfers_output_constraints
Optional parameters:
-h, --help show this help message and exit
-o OUTPUT_FILE specify output file (default:
SummarizeTransfers_output)
-t TRANSFER_CONFIDENCE_PERCENTAGE
specify a transfer confidence percentage value
(default: 100)
-m MAPPING_CONFIDENCE_PERCENTAGE
specify a mapping confidence percentage value
(default: 100)
-r RECIPIENT_CONFIDENCE_PERCENTAGE
specify a recipient confidence percentage value
(default: 100)
-c CUTOFF_VALUE specify a cutoff value to filter out transfers with
less confidence than cutoff (default: 1)
--internal show internal nodes only (default: False)
--quiet suppress process output (default: False)
--version show program's version number and exit
Description: Python 2 script that identifies and removes contradictions in timing constraints to produce a ranked species tree. See documentation in the MaxTiC manual. Note: MaxTiC.py is a Python 2 script.
Description: Python 3 script that combines the outputs of MaxTiC.py and SummarizeTransfers.py to produce a maximal consistent set of relative constraints with support values and file names.
Input: MaxTiC console output, MaxTiC list of constraints, SummarizeTransfers output file
$ python3 SummarizeMaxTiC.py MaxTiC_console MaxTiC_constraints SummarizeTransfers_output
Output: File of maximal consistent set of constraints
Description: Python 3 script that combines the outputs of SummarizeTransfers.py across mutliple runs using the same gene tree family inputs to produce a combined version of the outputs into one summary file.
Input: Directory of transfer files
$ python3 CombineTransfers.py transfer_dir
Output: File containing confident transfers across all input transfer files
Optional parameters:
-h, --help show this help message and exit
-o OUTPUT_FILE specify output file (default: CombineTransfers_output)
-c CONFIDENCE specify confidence percentage value (default: 100)
--version show program's version number and exit
- Alex Masi
This project is licensed under the MIT License - see the LICENSE.md file for details
- Thank you:
- Professor Mukul Bansal
- Soumya Kundu
- Eric Tannier
- Ranger-DTL
- MaxTiC
- ETE Toolkit
- Originally created at Professor Mukul Bansal's Computational Bio Lab at the University of Connecticut