alignment-distances(1)

✨ alignment-distances(1) ✨

okay bestie, this is the manual page for alignment-distances 💅 it's the tool that computes distances between alignments. no cap, it's giving precision 🔥

---

🌸 NAME

alignment-distances — computing distances between alignments. ✨

🦋 SYNOPSIS

alignment-distances analysis alignments-file1 [alignments-file2 ...]

💖 DESCRIPTION

okay so the whole point is to compute distances between alignments 🎀 that's literally it, but it's giving main character energy.

✨ INPUT OPTIONS ✨

• -h, –help — pull up a help message 🫶
• -s arg (=0), –skip arg (=0) — how many alignment samples to skip. default is 0 so nothing gets skipped unless you ask 🙈
• -m arg (=1000), –max arg (=1000) — the max number of alignments to analyze. default is 1000 🍓
• -V, –verbose — spills more log messages to stderr 📝
• –alphabet arg — pick your alphabet: DNA, RNA, Amino-Acids, Amino-Acids+stop, Triplets, Codons, or Codons+stop 🧚

💜 ANALYSIS OPTIONS ✨

• –distances arg (=splits:splits2:nonrecall:inaccuracy) — a colon-separated list of distances. this is the default list, lowkey iconic 👑
• –analysis arg — the analysis type: score, AxA, NxN, compare, median, distances 🌈
• –CI arg (=0.94999999999999996) — the confidence interval size. the default is 0.94999999999999996 🦋
• –mean — shows the mean and standard deviation 💅
• –median — shows the median and confidence interval ✨
• –minmax — shows the minimum and maximum distances 🔥

🎀 EXAMPLES ✨

okay so here are some examples, bestie 🫶

Compute distances from true.fasta to each in As.fasta:

% alignment-distances score true.fasta As.fasta

Compute distance matrix between all pairs of alignments in all files:

% alignment-distances AxA file1.fasta ... fileN.fasta

Compute all NxN pairwise alignment accuracies, averaged over As:

% alignment-distances NxN true.fasta As.fasta

Find alignment with smallest average distance to other alignments:

% alignment-distances median As.fasta A.fasta

Compare the distances with-in and between the two groups:

% alignment-distances compare A-dist1.fasta A-dist2.fasta

Report distribution of average distance to other alignments:

% alignment-distances distances As.fasta A.fasta

🚨 REPORTING BUGS 🚨

ngl this part is important, so read it twice 😭

for help, check the BAli-Phy online help at http://www.bali-phy.org/docs.php 🌸

please send bug reports to bali-phy-users@googlegroups.com 💌

👑 AUTHORS 👑

written by Benjamin Redelings 🫶

---

bestie, that's the whole page 🦋 this manual was brought to you by the alignment-distances(1) man page from the Feb 2018 release 🌈 you're literally so smart for reading this, periodt 💖✨