MIXR

MIXR curates orthologous gene alignments from combined genomic and transcriptomic datasets to produce high-quality multiple sequence alignments for comparative and evolutionary analyses.

Key Features:

• Systematic Parameter Analysis: Analyzes and applies parameters crucial for curating orthologous gene alignments to improve alignment quality.
• Advanced Pipeline for Combined Data: Processes combined transcriptomic and genomic data to generate accurate orthologous gene alignments.

Scientific Applications:

• Phylogenetic reconstruction of bats: Generated orthologous gene alignments for 18 bat species using transcriptome sequences of Hypsignathus monstrosus and Rousettus aegyptiacus combined with genomic data from 16 other bat species for tree construction and evolutionary study.
• Detection of positive selection: Enabled identification of 181 genes under positive natural selection in bats, with functions primarily associated with immune responses and collagen production.

Methodology:

Combining transcriptomic sequences with genomic data; systematic parameter-based curation of orthologous gene alignments; and phylogenetic assessment using the curated alignments.