ohdlf-pro 1.0.0

OHDLF-pro: a pipeline designed to filter and address orthologous gene heterogeneity, duplication, and loss

OHDLF-pro

Introduction

OHDLF-pro is the advanced evolution of the OHDLF pipeline, designed for high-performance phylogenomic analysis. Building upon OrthoFinder outputs, it automates the screening, alignment, and phylogenetic tree construction process with enhanced speed and accuracy.

Compared to the standard OHDLF, the Pro version introduces critical upgrades:

1. ⚡ Multi-threading Support: New parallel computing architecture (via the -t parameter) significantly accelerates BLAST filtering, alignment, and tree building steps.

2. ✨ Visual Progress Tracking: Integrated dynamic animations (progress bars) provide real-time feedback on current tasks and estimated completion time.

3. 🛡️ Robust Coalescence (Type 2): Now integrates DISCO (Decomposition of Species Trees) into the Coalescence workflow. This allows for the robust handling of multi-copy gene families, decomposing complex gene trees into single-copy orthologs to yield more statistically reliable species trees compared to simple filtering.

dependencies

• Biopython
• tqdm
• treeswift External Bioinformatics Tools (conda Recommended)

conda install -c bioconda iqtree aster blast raxml mafft

users can download the OHDLF.yaml file to directly configure the environment.

Install

pip install OHDLF-pro

Quick Start

Concatenation:
OHDLF-pro -l 0.05 -d 6 -s 97 -p 1 -t 8
Coalescence:
OHDLF-pro -l 0 -d 6 -s 97 -p 2 -t 8

Usage

OHDLF-pro.py -l [LOSS] -d [DUP] -s [SIM] -p [TYPE] -t [THREADS]


Commands:
  -l / --loss Allowable the max missing rate of gene. This option is required.
  -d / --duplication Allowable the max duplication number of gene. This option is required.
  -s / --similarity Allowable the similarity threshold of gene. If you do not set this parameter, the program will use '97' by default
  -p / --process_type process_type: 1 for Concatenation, 2 for Coalescence
  -t / --threads number of allowed threads

Input

Input :You need to 'cd' to the Orthofinder output directory named 'Results_XXX'. The software depends on two directories: 'Orthogroup_Sequences' and 'Orthogroups'.

Output

Type 1 (Concatenation)

• final_OrthologsAlign_GDL.phy: The concatenated alignment (phy file).

• RAxML_bestTree.OHDLF_tree: The final Maximum Likelihood tree.

Type 2 (Coalescence with DISCO)

• GDL_Orthologue_Sequences_iqtree: Individual gene trees inferred by IQ-TREE.

• GDL_Orthologue_Sequences_DISCO: Decomposed gene trees processed by DISCO (Multi-copy -> Single-copy).

• all_disco.trees: The combined input file for ASTRAL.

• OHDLF_DISCO_ASTRAL.nwk: The final, robust species tree.