esl-alipid

name	esl-alipid
description	Use when calculating pairwise percent identities from multiple sequence alignments in FASTA or Stockholm format.
disable-model-invocation	true
user-invocable	true

esl-alipid

Quick Start

• Command: esl-alipid [options] <alignment_file>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/esl-alipid
• Full reference: See references/help.md for complete options and usage

When To Use This Tool

• Use esl-alipid when you need pairwise percent-identity measurements across all sequence pairs in an alignment.
• It is useful for diagnosing redundancy, alignment diversity, and whether an MSA should be clustered, filtered, or split before downstream modeling.
• Use it on aligned sequence files, not raw unaligned FASTA collections.
• In this environment the binary is currently blocked by the missing libopenblas.so.0, so treat the syntax below as documented behavior pending library repair.

Common Patterns

# Compute pairwise percent identities for an alignment
esl-alipid alignment.sto

# Suppress the header in machine-oriented output
esl-alipid --noheader alignment.sto

# Force alphabet interpretation if guessing is ambiguous
esl-alipid --amino alignment.sto
esl-alipid --dna alignment.sto

Recommended Workflow

1. Prepare a multiple sequence alignment file (FASTA or Stockholm format)
2. Run esl-alipid <alignment_file> to compute pairwise PIDs
3. Review output to assess sequence diversity or redundancy
4. Use results to guide filtering, clustering, or downstream analysis decisions

Guardrails

• Ensure input file is a valid multiple sequence alignment (not unaligned sequences)
• Verify library dependencies are available (requires libopenblas)
• Check that all sequences in the alignment use the same alphabet
• If automatic alphabet detection fails, force the correct alphabet with --amino, --dna, or --rna