(Under Construction) FastDTLmapper: Fast genome-wide DTL event mapper

Table of contents

• Overview
• Install
• Pipeline Summary
• Command Usage
• Output Contents

Overview

Gene gain/loss is considered to be one of the most important evolutionary processes driving adaptive evolution, but it remains largely unexplored. Therefore, to investigate the relationship between gene gain/loss and adaptive evolution in the evolutionary process of organisms, I developed a software pipeline FastDTLmapper which automatically estimates and maps genome-wide gene gain/loss.
FastDTLmapper takes two inputs, 1. Species tree (Newick format) 2. Genomic CDSs (Fasta|Genbank format), and performs genome-wide mapping of DTL(Duplication-Transfer-Loss) events by DTL reconciliation of species tree and gene trees.

Fig. Genome-wide gain/loss map result example (all_gain_loss_map.png)
Each nodes gain/loss data is mapped in following format (NodeID | GeneCount [gain=GainCount los=LossCount])
Map data is embeded in newick format bootstrap value field and user can visualize using SeaView.

Install

FastDTLmapper is implemented in Python3(>=3.7) and runs on Linux (Tested on Ubuntu20.04).

Install PyPI stable version with pip:

pip install fastdtlmapper

Install latest development version with pip:

pip install git+git://github.com/moshi4/FastDTLmapper.git

Dependencies

All of the following dependencies are packaged in src/fastdtlmapper/bin directory.

• OrthoFinder
  Orthology inference tool
• mafft
  Sequences alignment tool
• trimal
  Alignment sequences trim tool
• IQ-TREE
  Phylogenetic tree reconstruction tool
• AnGST
  DTL reconciliation tool (Requires Python 2.X to run)
• parallel
  Job parallelization tool (Requires Perl to run)

Pipeline Summary

1. Grouping ortholog sequences using OrthoFinder
2. Align each OG(Ortholog Group) sequences using mafft
3. Trim each OG alignment using trimal
4. Reconstruct each OG gene tree using IQ-TREE
5. Species tree & each OG gene tree DTL reconciliation using AnGST
6. Aggregate and map genome-wide DTL reconciliation result

Command Usage

Run Command

FastDTLmapper -i [fasta|genbank directory] -t [species tree file] -o [output directory]

Options

-h, --help           show this help message and exit
-i , --indir         Input Fasta(*.fa|*.faa|*.fasta), Genbank(*.gb|*.gbk|*.genbank) directory
-t , --tree          Input rooted species tree file (Newick format)
-o , --outdir        Output directory
-p , --process_num   Number of processor (Default: MaxProcessor - 1)
--dup_cost           Duplication event cost (Default: 2)
--los_cost           Loss event cost (Default: 1)
--trn_cost           Transfer event cost (Default: 3)
--inflation          MCL inflation parameter (Default: 3.0)
--timetree           Use species tree as timetree (Default: off)
--rseed              Number of random seed (Default: 0)

Input Limitation

• fasta or genbank files (--indir option)
  Following characters cannot be included in file name '_', '-', '|', '.'
• species tree file (--tree option)
  Species name in species tree must match fasta or genbank file name

Timetree Option

If user set this option, input species tree must be ultrametric tree.
--timetree enable AnGST timetree option below (See AnGST manual for details).

If the branch lengths on the provided species tree represent times, AnGST can restrict the set of possible inferred gene transfers to only those between contemporaneous lineages

Example Command

FastDTLmapper -i ./example/fasta/ -t ./example/species_tree.nwk -o ./fastdtlmapper_result

Output Contents

Output Top Directory

Output Directory Structure & Files

.
├── 00_user_data/  -- User input data
│   ├── fasta/     -- Formatted fasta files
│   └── tree/      -- Formatted newick species tree files
│
├── 01_orthofinder/  -- OrthoFinder raw output results
│
├── 02_dtl_reconciliation/  -- Each OG(Ortholog Group) DTL reconciliation result
│   ├── OG0000000/
│   │   ├── OG0000000.fa                 -- OG fasta file
│   │   ├── OG0000000_aln.fa             -- OG alignment fasta file
│   │   ├── OG0000000_aln_trim.fa        -- Trimmed OG alignement fasta file
│   │   ├── OG0000000_dtl_map.nwk        -- OG DTL event mapped tree file
│   │   ├── OG0000000_gain_loss_map.nwk  -- OG Gain-Loss event mapped tree file
│   │   ├── angst/                       -- AnGST DTL reconciliation result
│   │   └── iqtree/                      -- IQ-TREE gene tree reconstruction result
│   │
│   ├── OG0000001/
│   . 
│   . 
│   └── OGXXXXXXX/
│
├── 03_aggregate_map_result/  -- Genome-wide DTL reconciliation aggregated and mapped results
│   ├── all_dtl_map.nwk              -- Genome-wide DTL event mapped tree file
│   ├── all_gain_loss_map.nwk        -- Genome-wide Gain-Loss event mapped tree file
│   ├── all_og_node_event.tsv        -- All OG DTL event record file
│   ├── all_transfer_gene_count.tsv  -- All transfer gene count file
│   └── all_transfer_gene_list.tsv   -- All transfer gene list file
│
└── log/
    ├── parallel_cmds/ -- Parallel run command log results
    └── run_config.log -- Program run config log file