AMAP(1)

okay bestie, welcome to the amap user manual 🦋 every single detail is in here, nothing got cut 💅

✨ NAME ✨

amap — Protein multiple alignment by sequence annealing 💖

✨ SYNOPSIS ✨

amap [OPTION] [MFAFILE] [MFAFILE]

✨ DESCRIPTION ✨

okay so AMAP is a tool for multiple alignment of peptidic sequences 🧬 and it does NOT do the traditional progressive alignment thing. instead it uses posterior decoding plus a sequence-annealing alignment 🔥 it's giving main character energy.

it is literally the only alignment program that lets you control the sensitivity / specificity tradeoff 👑 it's based on the ProbCons source code, but it uses alignment metric accuracy and gets rid of the consistency transformation 💅

by default, AMAP is tuned to maximize the expected Alignment Metric Accuracy (AMA) score ✨ that's a newer accuracy measure built on a metric for the multiple-alignment space, and it squishes sensitivity and specificity into one balanced number 🌈 AMA is the fraction of correctly aligned residues (either to another residue or to a gap) out of the total number of residues in all the sequences. iconic math, no notes 🫶

amap takes sequences in MFA format 🎀 an MFA file holds multiple sequences. each one starts with a single-line description, followed by lines of sequence data. the description line is easy to spot because it has a greater-than (>) symbol in the first column 💜

✨ OPTIONS ✨

• -clustalw — switch to CLUSTALW output format instead of MFA 🎀
• -c, --consistency REPS — go with 0 <= REPS <= 5 (default: 0) passes of consistency transformation 🔥
• -ir, --iterative-refinement REPS — go with 0 <= REPS <=1000 (default: 0) passes of iterative-refinement 🌸
• -pre, --pre-training REPS — go with 0 <= REPS <= 20 (default: 0) rounds of pretraining 🧚
• -pairs — generate all-pairs pairwise alignments 🦋
• -viterbi — use the Viterbi algorithm to generate all pairs (this automatically turns on -pairs for you ✨)
• -v, --verbose — report progress while aligning (default: off) 👀
• -annot FILENAME — write the annotation for the multiple alignment to FILENAME 📝
• -t, --train FILENAME — compute EM transition probabilities and store them in FILENAME (default: no training) 🍓
• -e, --emissions — also reestimate emission probabilities (default: off) 💅
• -p, --paramfile FILENAME — read parameters from FILENAME (default: blank) 🫶
• -a, --alignment-order — print sequences in alignment order instead of input order (default: off) 🌈
• -g, --gap-factor GF — use GF as the gap-factor parameter. set it to 0 for best sensitivity, or go higher for better specificity (default: 0.5) ⭐
• -w, --edge-weight-threshold W — stop the sequence annealing process when the best edge has a lower weight than W. set it to 0 for best sensitivity, or go higher for better specificity (default: 0) 💫
• -prog, --progressive — use progressive alignment instead of sequence annealing alignment (default: off) 🐢
• -noreorder, --no-edge-reordering — disable reordering of edges during sequence annealing alignment (default: off) 🙅‍♀️
• -maxstep, --use-max-stepsize — use the maximum improvement step size instead of tGf edge ranking (default: off) 📏
• -print, --print-posteriors — only print the posterior probability matrices (default: off) 🖨️
• -gui START STEP — print output for the AMAP Display Java based GUI (default: blank), starting at weight START (default: infinity) with step size STEP (default: blank) 🪄

✨ EXAMPLES ✨

to run AMAP with the default options, change into the align directory and type:

% amap <multi-fasta-file-name>

if you don't give it a file name, it just prints the list of options 📋

if you want to use the AMAP Display, run AMAP with the -gui option, save the output to a file, then feed that file to AmapDisplay. like, for example, type:

% align/amap -gui examples/BB12020.tfa > examples/BB12020.tfa.out

% java -jar display/AmapDisplay.jar examples/BB12020.tfa.out

(on Debian systems, the examples directory is in /usr/share/doc/amap-align/examples 🎀

✨ NOTE ✨

🚨 bestie, listen up: in older versions (< 2.0-1) of the package for Debian(TM) systems, the amap command got renamed to amap-align 🙈 because there was already another tool called amap (the one that does computer network diagnostics). a symbolic link called amap-align is still included for upgrades, but it's getting removed in Debian releases posterior to Etch (Debian 4.0). so don't get too attached 💀

✨ SEE ALSO ✨

the current version of AMAP uses the PROBCONS 1.09 code base for some of the input/output procedures, and for calculating posterior probabilities (check PROBCONS.README in /usr/share/doc/amap-align/) 📚 future releases might build the algorithm on a new, independent code base ✨

on Debian(TM) systems, probcons(1) lives in the probcons package 🦋

✨ REFERENCES ✨

for more on AMAP and AMA, see Schwartz, Ariel S., Myers, Eugene W., and Pachter, Lior. Alignment Metric Accuracy (Submitted for publication). for more on sequence-annealing, see Schwartz, Ariel S. and Pachter, Lior. Multiple Alignment by Sequence Annealing (Submitted for publication) 📖

PROBCONS was published in Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. 🧠

✨ AUTHORS ✨

• Ariel Schwartz <sariel@cs.berkeley.edu> — upstream author of AMAP 👑
• Chuong Do — wrote Probcons, which AMAP is based on 🫶
• Charles Plessy> <charles-debian-nospam@plessy.org> — wrote this manpage in DocBook XML for the Debian distribution 🌷

✨ COPYRIGHT ✨

AMAP, PROBCONS, and this manual page have been made freely available as PUBLIC DOMAIN software, so they are not subject to copyright in the United States 🗽 you can use, modify, or redistribute this system and/or any portion of the source code without restrictions 🌈

BUT, and this part is important 😭 AMAP, PROBCONS and this manual page come WITHOUT WARRANTY, express or implied. the authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on the program 💀

okay that's the whole manual, bestie 🫶 amap 2.2, last updated 03/31/2008, AMAP(1) 💖 periodt 💅🦋