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Title: ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees
Abstract Motivation

Species tree inference from multi-copy gene trees has long been a challenge in phylogenomics. The recent method ASTRAL-Pro has made strides by enabling multi-copy gene family trees as input and has been quickly adopted. Yet, its scalability, especially memory usage, needs to improve to accommodate the ever-growing dataset size.

Results

We present ASTRAL-Pro 2, an ultrafast and memory efficient version of ASTRAL-Pro that adopts a placement-based optimization algorithm for significantly better scalability without sacrificing accuracy.

Availability and implementation

The source code and binary files are publicly available at https://github.com/chaoszhang/ASTER; data are available at https://github.com/chaoszhang/A-Pro2_data.

Supplementary information

Supplementary data are available at Bioinformatics online.

 
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Award ID(s):
1845967
PAR ID:
10372216
Author(s) / Creator(s):
; ;
Publisher / Repository:
Oxford University Press
Date Published:
Journal Name:
Bioinformatics
ISSN:
1367-4803
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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