alistat(1)

✨ alistat(1) — the alignment stats queen 👑

okay bestie, let's talk about alistat, the tool that tells you everything about a multiple alignment file 💅 it's giving statistics, and it's giving them in a way that's actually useful 🦋

💖 NAME

alistat — show statistics for a multiple alignment file 🎀

🧚 SYNOPSIS

alistat [options] alignfile

🌸 DESCRIPTION

okay so alistat reads a multiple sequence alignment from the file alignfile in literally any supported format (including SELEX, GCG MSF, and CLUSTAL) 🫶 then it spills a bunch of simple stats tea ☕ the stats include the name of the format, the number of sequences, the total number of residues, the average and range of the sequence lengths, and the alignment length (which counts gap characters too) 📏

now the percent identity stuff is where it gets spicy 🌶️ a percent pairwise alignment identity is defined as (idents / MIN(len1, len2)), where idents is the number of exact identities and len1, len2 are the unaligned lengths of the two sequences 🔥

the "average percent identity", "most related pair", and "most unrelated pair" are the average, maximum, and minimum of all (N)(N-1)/2 pairs, respectively 💜

and the "most distant seq" is calculated by finding the maximum pairwise identity (best relative) for all N sequences, then finding the minimum of those N numbers. so basically it's the most outlying sequence, the lowkey loner of the group 🥺💀

🎀 OPTIONS

• -a — show extra verbose info! 🔍 you get a table with one line per sequence showing the name, length, and its highest and lowest pairwise identity. every line gets a * prefix so you can grep and sort them easily 🧹 for example, alistat -a foo.slx | grep * | sort -n +3 gives you a ranked list of the most distant sequences in the alignment 👑 incompatible with the -f option, so don't try to mix them bestie 🙅‍♀️
• -f — fast mode! ⚡ it uses a sampling method to estimate the average %id. when you pick this one, alistat doesn't show the other three pairwise identity numbers 🫠 it's super useful for very large alignments where calculating all (N)(N-1) pairs would be prohibitive (like Pfam's GP120 alignment with over 10,000 sequences) 🌈 incompatible with the -a option 🙅‍♀️
• -h — print brief help 📖 includes the version number and a summary of all options, including expert options 🧠
• -q — be quiet 🤫 suppresses the verbose header (program name, release number and date, and the parameters and options in effect) 🔇
• -B — babelfish mode 🐟 autodetects and reads a sequence file format other than the default (FASTA). almost any common format is recognized, including Genbank, EMBL, SWISS-PROT, PIR, and GCG unaligned sequence formats, plus Stockholm, GCG MSF, and Clustal alignment formats 📚 see the printed documentation for a complete list of supported formats 💅

🦋 EXPERT OPTIONS

• --informat <s> — tell it the sequence file is in format s instead of the default FASTA 🎯 common examples include Genbank, EMBL, GCG, PIR, Stockholm, Clustal, MSF, or PHYLIP, and the printed documentation has the full list of accepted names 📜 this one overrides both the default FASTA format and the -B babelfish autodetection 👑

🌈 SEE ALSO

afetch(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), stranslate(1), weight(1) 🫶

💜 AUTHOR

Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine 🎓 freely distributed under the GNU General Public License (GPL) ⭐ see COPYING in the source code distribution for more details, or contact me 💌

Sean Eddy HHMI/Department of Genetics Washington University School of Medicine 4444 Forest Park Blvd., Box 8510 St Louis, MO 63108 USA Phone: 1-314-362-7666 FAX : 1-314-362-2157 Email: eddy@genetics.wustl.edu

bestie, that's the whole tea ☕🦋 Biosquid 1.9g, January 2003, you literally cannot be stopped now 💅✨