ANALYSESEQS(1)

💖 ANALYSESEQS(1) 💖

General Commands Manual

✨ NAME ✨

AnalyseSeqs - Analyse a set of sequences of common length 🦋

👑 SYNOPSIS 👑

AnalyseSeqs [-X[bswn]] [-Q] [-M{mask}[+|!]] [-D{H|A|G}] [-d{S|H|D|B}]

🌸 DESCRIPTION 🌸

okay so AnalyseSeqs reads a set of sequences from stdin and tries a bunch of different sequence analysis methods on them 💅 The ones it currently offers are:

• Statistical geometry for quadruples of sequences. Heads up, this one is PRELIMINARY and NOT WELL TESTED BY NOW 😭
• Split decomposition ✨
• Neighbour joining and Ward's variance method for reconstructing phylogenies using various distance measures 🌳

For statistical geometry and the cluster methods, you can get PostScript output 🎀

The program keeps reading until it runs into one of the separator characters @ or %. Only sequences made of alphabetical characters (or of a specified alphabet) get processed, and everything else gets ignored 🙈 It stops reading if it hits an EOF condition, or if there's no valid sequence data between two lines that start with separator characters.

You can also drop a list of taxa names into the input stream! 🧚 The list starts with a line beginning with *. Optionally, you can put a file name prefix [fn] for the PostScript output on that same line. The entries look like x : Taxon, where x is the number of the taxon, i.e., the matching entry in the list of input sequences. The taxa list doesn't have to be complete, but it must end with a line beginning with * or any of the separator characters. The taxa list gets printed on top of the output, and the names are used as labels in the PostScript output 💜

🦋 OPTIONS 🦋

• -X[bswn] — this is how you pick which analysis methods you want 👑 Here's the menu:
  • [b] — Statistical Geometry. It makes a PostScript file called [fn_]box.ps with a graphical representation of the statistical geometry. The resulting box is a great measure of "tree likeness" for your data set 🔥 This is the default, obviously.
  • [s] — Split decomposition 💅
  • [w] — Cluster analysis using Ward's method. It creates a PostScript file called [fn_]wards.ps with a drawing of the tree 🌈
  • [n] — Cluster analysis using Saitou's neighbour joining method. It creates a PostScript file called [fn_]nj.ps with a drawing of the tree ⭐
• -Q — this one's a whole vibe 💖 It means you want a statistical geometry analysis comparing four data sets, like if you're trying to confirm the significance of a proposed phylogeny. It's only useful for statistical geometry, so the -X option gets ignored here. Each of the four data sets has to look like this, where number is 1, 2, 3, or 4 for the four groups you're comparing:

* [filename_prefix]
# number
[list of taxa names]
*
list of sequences
%

• -M{mask}[+|!] — lets you set a mask for the input file 🎀 The {mask} is either one of the letters below (for a predefined alphabet) or a % sign followed by all the characters you want accepted. A + at the very end of the mask makes the input case sensitive. By default, the input gets converted to upper case. A ! can be used to convert the input to RY code: GgAaXx -> R, UuCcKkTt -> Y, and all other letters become * 🦋
  • -Ma — all letters A-Z and a-z 🔤
  • -Mu — uppercase letters 🔠
  • -Ml — lowercase letters 🔡
  • -Mc — digits [0-9] 🔢
  • -Mn — all alphanumeric characters 🫶
  • -MR — RNA alphabet (GCAUgcau) 🧬
  • -MD — DNA alphabet (GCATgcat) 🧬
  • -MA — amino acids in one-letter code 🍓
  • -MS — secondary structures coded as '^.()' 🌙
  • -M%alphabet — use the alphabet you specify yourself ✨
• -D — picks the algorithm used to calculate the distance matrix for your input data set. Your options are:
  • -DH — Hamming Distance 💜
  • -DA[,cost] — simple alignment distance according to Needleman and Wunsch 🌸 You can put a gap cost other than 1. after the comma.
  • -DG[,cost1,cost2] — Gotoh's distance with gap cost function g(k) = cost2+cost1*(k-1). cost2<=cost1 has to be true. The defaults are cost1=1. and cost2=1., which gives the same distance as option A 💅

CAUTION bestie: ONLY THE HAMMING DISTANCE IS WELL TESTED BY NOW !!!

• -d — picks the edit cost matrix to use. Your options are:
  • -dS — simple distance. Indels and substitutions of different characters all cost 1. You can change the indel cost by setting the gap costs with the algorithm options -DA and -DG. This is the default ✨
  • -dH — a distance matrix for RNA secondary structures, inspired by Hogeweg's similarity measure (J.Mol.Biol 1988) 🌈 The gap function gets set automatically.
  • -dD — Dayhoff's matrix for amino acid distances 🍓
  • -dB — distinguishes purines and pyrimidines only 🌙

CAUTION: this one only affects the calculation of distances. It does NOT affect the computation of the statistical geometry, which is done directly on the sequences. If you want statistical geometry on RY sequences, use the ! sign with the -M option, for instance -MR! 🙈

📚 REFERENCES 📚

The method of statistical geometry was introduced by M. Eigen, R. Winkler-Oswatitsch and A.W.M. Dress (Proc Natl Acad Sci, 85:1988,5912). 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 is the beta test version! Some options or combinations of options may still produce nonsense 💀 Please send bug reports to ivo@tbi.univie.ac.at.

🎀 VERSION 🎀

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

🧚 AUTHOR 🧚

Peter F Stadler, Ivo L. Hofacker. The real ones 👑

🐛 BUGS 🐛

Comments should be sent to ivo@itc.univie.ac.at.

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