analyse-seqs

name	analyse-seqs
description	Use when analyzing equal-length sequence sets with the legacy ViennaRNA statistical-geometry, clustering, or distance-matrix utility driven from stdin.
disable-model-invocation	true
user-invocable	true

analyse-seqs

Legacy ViennaRNA sequence-set analysis tool for equal-length inputs. It reads sequence blocks from stdin, can build Hamming or edit-distance matrices, and can emit PostScript summaries for statistical geometry or tree reconstruction modes.

Quick Start

• Command: AnalyseSeqs
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/AnalyseSeqs
• Live help path: AnalyseSeqs -h
• Input contract: reads sequence data from stdin until a separator line beginning with @ or %

When To Use This Tool

• Analyze a set of equal-length sequences with legacy ViennaRNA exploratory methods rather than modern aligners or phylogeny suites.
• Build Hamming, Needleman-Wunsch, or Gotoh distance matrices before neighbour-joining or Ward clustering.
• Generate statistical-geometry or clustering PostScript output from a small curated sequence panel.
• Work from stdin streams that may also include an optional taxa list and output filename prefix.

Common Patterns

# 1) Neighbour-joining with Hamming distance and taxa labels
cat <<'EOF' | AnalyseSeqs -Xn -DH
* demo
1 : A
2 : B
3 : C
4 : D
*
AAAA
AAAT
AATT
TTTT
@
EOF

# 2) Statistical geometry (the default -Xb mode) with a PostScript sidecar
cat <<'EOF' | AnalyseSeqs -Xb -DH
* demo
1 : A
2 : B
3 : C
4 : D
*
AAAA
AAAT
AATT
TTTT
@
EOF
# writes demo_box.ps

# 3) Ward clustering with a generated PostScript tree
cat <<'EOF' | AnalyseSeqs -Xw -DH
* demo
1 : A
2 : B
3 : C
4 : D
*
AAAA
AAAT
AATT
TTTT
@
EOF
# writes demo_wards.ps

Recommended Workflow

1. Prepare equal-length sequences and terminate the input block with @ or %.
2. If you want labeled output files, prepend a taxa block starting with * prefix, followed by numbered n : Taxon lines and a closing *.
3. Choose the analysis family with -X... and the distance algorithm with -D...; use -d... only when you intentionally want a non-default edit-cost matrix.
4. Inspect both stdout summaries and any generated PostScript sidecars such as *_box.ps, *_nj.ps, or *_wards.ps.

Guardrails

• The real binary name is capitalized: AnalyseSeqs, not analyse-seqs.
• -h, --help, and --version all fell through to the same usage text in live testing; no clean version banner was observed.
• The installed man page says the tool reads from stdin until it sees @ or %, ignores unrelated non-sequence lines, and supports an optional taxa list beginning with *.
• A minimal two-sequence smoke test (AAAA, AAAT, @) exited 0 with no stdout or sidecar output, so do not expect every input size to yield a direct report.
• The man page explicitly warns that only Hamming distance is well tested; treat -DA and -DG as higher-risk legacy paths.
• Generated PostScript filenames derive from the taxa-list prefix and analysis mode, for example demo_box.ps, demo_nj.ps, and demo_wards.ps.