PROALIGN(1)

💖 PROALIGN 💖

okay bestie, gather round, because this is the manual page for proalign — a probabilistic multiple alignment program — and it lives in the User Commands section of the manual. she's giving serious bioinformatics main character energy and honestly? we're obsessed. 🧬✨

🌸 NAME 🌸

proalign — a probabilistic multiple alignment program 🦋

✨ SYNOPSIS ✨

proalign [OPTIONS]

🎀 DESCRIPTION 🎀

okay so real talk: from the command line you only get limited usage of the program. no cap. if you want the full experience, use the version with the GUI — which, iconic behaviour btw, you start by just running it without any OPTIONS. 💅

bestie listen: no options = GUI. options = command line, but only limited usage. that's the whole vibe check.

💜 OPTIONS 💜

• -nogui — force command line mode. she said no GUI today, we're doing this raw. 💀
• -seqfile=<sequence file> — point her at your sequence file. 🍓
• -treefile=<tree file> — point her at your tree file. 🌸
• -newtree — compute a new guide tree. fresh tree, fresh me. 🌱
• -sample — sample the traceback path. if you don't pass this, Viterbi is chosen instead. iykyk. ✨
• -delta=<HMM delta> or -delta=estimate — set the HMM delta. if you don't give it, the default is used. 🫶
• -epsilon=<HMM epsilon> or -epsilon=estimate — set the HMM epsilon. if you don't give it, the default is used. 🫶
• -gapfreq=<gap frequency> — the gap frequency. if you don't give it, the default is used. 💫
• -gapprob=<gap substitution probability> — the gap substitution probability. if you don't give it, the default is used. 💫
• -bwidth=<search band width> — the search band width. if you don't give it, the default is used. 🔍
• -distscale=<distance scale factor> — the distance scale factor, specifically for branch lengths. 🌿
• -nocorrection — no correction for pairwise distances when computing the guide tree. skipping the glow-up, respectfully. 🙈
• -notrailing — no trailing sequence correction. 🚫
• -trailing=<trailing sequence correction length> — set the trailing sequence correction length, for missing ends. 🎀
• -penalize=true, or =false — penalize end gaps on pairwise alignments for the guide tree. yes or no, pick your fighter. ⚔️
• -writemean — write the mean posterior probability of sites. 📊
• -writeall — write the posterior probability of each node. 🌈
• -writeroot — write the root node character probabilities. the root said let me speak. 👑
• -wag — use the WAG probability table. 🧬
• -dayhoff — use the Dayhoff probability table. 🧬
• -jtt — use the JTT probability table. 🧬
• -outfile=<alignment file> — where your alignment gets written. 🍓
• -outformat=pir, -outformat=msf, -outformat=phylip, or -outformat=nexus — pick your output format, bestie. four flavours, all slay. 💅
• -quiet — no log. she's not narrating today. 🤫

and that's the whole page, no notes, ate and left no crumbs. 💖

this one's from ProAlign, dated May 2013, and it lives under PROALIGN(1) in the manual. mwah, love u, go align something iconic. 🎀✨🦋