Gotree

Gotree provides command-line operations for manipulating phylogenetic trees and multiple sequence alignments for bioinformatics analyses.

Key Features:

• Command set: Implements over 120 commands covering multiple sequence alignment and phylogenetic tree manipulations.
• API: Provides a programmatic API specifically tailored for multiple sequence alignment and phylogenetic tree operations.
• File reformatting: Performs file reformatting for tree and alignment data.
• Sequence renaming: Supports renaming of sequences in alignments and trees.
• Tree re-rooting: Supports re-rooting of phylogenetic trees.
• Tree comparison: Performs comparisons between phylogenetic trees.
• Bootstrap support computation: Computes bootstrap support values for phylogenetic trees.
• Implementation and parallelization: Implemented in the Go programming language with support for parallel execution when applicable.

Scientific Applications:

• Phylogenetic analysis: Manipulation and analysis of phylogenetic trees and associated multiple sequence alignments.
• Support assessment: Computation of bootstrap supports to assess node confidence in phylogenies.
• Comparative phylogenomics: Comparison and validation of alternative phylogenetic trees.

Methodology:

Implements over 120 commands and an API in the Go language to perform file reformatting, sequence renaming, tree re-rooting, tree comparison, and bootstrap support computation, with support for parallel execution when applicable.