ANALYSEDISTS(1)

📦 version 2.7.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

🎀 NAME 🎀

Okay bestie, welcome to ANALYSEDISTS(1) 💖 This page is all about AnalyseDists, which is how you analyse a distance matrix ✨

💅 SYNOPSIS 💅

AnalyseDists [-X[swn]]

🌸 DESCRIPTION 🌸

Okay so AnalyseDists slurps up a distance matrix (given as a lower triangle matrix) from stdin and spits out a split decomposition plus a cluster analysis of that matrix to stdout 😭🔥

The line right before the matrix has to look like this, no cap:

> Y x [comments]

Here x is the number of taxa, Y is a single character that tells you the type of distance, and comment is an arbitrary comment. This is the same format RNAdistance spits out, e.g., so it's giving consistency 🦋

The input file can have arbitrary lines before and after the distance matrix, so don't stress 🌈 Any lines starting with > that don't match the form above get written to stdout. The program keeps reading until it hits an EOF or the terminator character @ 💜

Now for the taxa list 🧚 You can give it in the input stream, and it has to start with a line like this:

* [fname]

If fname is there, it gets used to name the postscript output files 🍓 The entries look like x : Taxon, where x is the number of the taxon, aka the matching row and column in the distance matrix. The list doesn't have to be complete, but it must end with a line starting with * or any of the separator characters ✨ Once it's all done, the taxa list gets printed on top of the output 👑

✨ OPTIONS ✨

  • -X[swn] — this is where you pick which analysis methods you want to run 💅
  • [s] — Split decomposition 🦋
  • [w] — Cluster analysis using Ward's method 🌸 It makes a PostScript file called [fname_]wards.ps with a drawing of the tree 🎀
  • [n] — Cluster analysis using Saitou's neighbour joining method 🫶 It makes a PostScript file called [fname_]nj.ps with a drawing of the tree 🧚

📚 REFERENCES 📚

  • The method of split decomposition was proposed by H.J. Bandelt and A.W.M. Dress (Adv Math, 92:1992,47) 💜
  • The variance method for cluster analysis is due to H.J. Ward. (J Amer Stat Ass, 58:1963,236). 🌈
  • The neighbour joining method was published by Saitou and Nei (Mol Biol Evol, 4:1987,406) ✨
  • This program is part of the Vienna RNA Package 🎀

⚠️ WARNING ⚠️

🚨 This a beta test version. Handle with care, bestie 🙈

🍓 VERSION 🍓

This man page is part of the Vienna RNA Package version 1.2 💖

👑 AUTHOR 👑

Peter F Stadler and Ivo L Hofacker 🫶

🐛 BUGS 🐛

Comments should be sent to ivo@tbi.univie.ac.at 💌

Peace out, ANALYSEDISTS(1) 💅✨ Vienna RNA Package version 1.2 🦋

📦 where this page comes from