PHASTODDS(1)

👑 PHASTODDS(1) — User Commands, section 1 👑

okay so bestie, welcome to the manual page for phastOdds, and no cap, it's a whole vibe. it's in the User Commands part of the manual (that's the (1) — iykyk). let's get into it 💅

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🦋 NAME 🦋

phastOdds — compute log-odds scores based on two phylogenetic models or phylo-HMMs, ✨

(yes the original sentence really does end in a comma. iconic. we're keeping it.)

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🌸 DESCRIPTION 🌸

okay so the whole point: this computes log-odds scores based on two phylogenetic models or phylo-HMMs — one for the features you actually care about (think coding exons, conserved regions, the main characters) and one for background (the supporting cast). 🫶

and then it does one of these three things:

1. compute a score for each feature in an input set, and output the same set of features with scores; or
2. output a separate score for each position in fixed-step WIG format (http://genome.ucsc.edu/goldenPath/help/wiggle.html); or
3. compute scores in a sliding window of designated size, and output a three-column file, with the index of the center of each window followed by the score for that window on the positive strand, then the score for that window on the negative strand. 🌈

and here's the default tea, so listen up: by default it assumes a reference sequence alignment, with the reference sequence appearing first. feature coordinates are assumed to be defined with respect to the reference sequence (peep --refidx for that one 👀).

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✨ SYNOPSIS ✨

phastOdds [OPTIONS] --background-mods <bmods> [--background-hmm <bhmm>]
--feature-mods <fmods> [--feature-hmm <fhmm>] ( --features <feats> |
--window <size> ) <alignment>

and now the deets on those arguments, because they matter fr fr:

• <bmods> and <fmods> should be comma-delimited lists of phylogenetic models in .mod format (as produced by phyloFit)
• <feats> may be in GFF, BED, or genepred format
• <alignment> may be in FASTA format or an alternative format specified by --msa-format
• HMM files should be in the format used by exoniphy 🌸

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🎀 EXAMPLE 🎀

(and yes, there's more on the options further down 👇)

1. conservation scores for features, GFF edition 🧚

compute conservation scores for features in a GFF file, based on a model for conserved sites (conserved.mod) vs. a model of neutral evolution (neutral.mod). (these models may be estimated with phyloFit or phastCons.)

phastOdds --background-mods neutral.mod --feature-mods conserved.mod --features features.gff alignment.fa > scores.gff

and bestie, features could alternatively be specified in BED or genepred format — the format will be auto-recognized, which is giving low-effort-on-your-part in the best way. the program can be made to produce BED-formatted output with --output-bed. 💅

2. sliding window, size 100 🪟

compute conservation scores in a sliding window of size 100.

phastOdds --background-mods neutral.mod --feature-mods conserved.mod --window 100 alignment.fa > scores.dat

(a couple notes: the window is advanced one site at a time. window boundaries are defined in the coordinate frame of the multiple alignment, but center coordinates are converted to the frame of the reference sequence as they are output. okay so it's a whole coordinate glow-up, periodt.)

3. coding potential, phylo-HMM edition 🧬

compute a "coding potential" score for features in a BED file, based on a phylo-HMM for coding regions versus a phylo-HMM for noncoding DNA, with states for conserved and nonconserved sequences.

phastOdds --background-mods codon1.mod,codon2.mod,codon3.mod --background-hmm coding.hmm --feature-mods neutral.mod,conserved-noncoding.mod --feature-hmm noncoding.hmm --features features.bed --output-bed alignment.fa > scores.bed

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💅 OPTIONS 💅

• --background-mods, -b <backgd_mods> — (Required) comma-delimited list of tree model (*.mod) files for background. if you use this with --background-hmm, the order of models must correspond to the order of states in the HMM. no mixing that up bestie, the order is the whole plot 🙈
• --background-hmm, -B <backgd.hmm> — the HMM for background. if there is only one backgound tree model, a trivial (single-state) HMM will be assumed. (that's a single-state HMM doing its little solo moment ✨)
• --feature-mods, -f <feat_mods> — (Required) comma-delimited list of tree model (*.mod) files for features. if you use it with --feature-hmm, the order of models must correspond to the order of states in the HMM. same rule, same energy 👑
• --feature-hmm, -F <feat.hmm> — the HMM for features. if there is only one tree model for features, a trivial (single-state) HMM will be assumed. 🌸
• --features, -g <feats.gff> — (Required unless -w or -y) file defining features to be scored (GFF, BED, or genepred). pick your fighter 💖
• --window, -w <size> — (can be used instead of -g or -y) compute scores in a sliding window of the specified size. 🪟
• --base-by-base, -y — (can be used instead of -g or -y) output base-by-base scores, in the coordinate frame of the reference sequence (or of the sequence specified by --refidx). output is in fixed-step WIG format (http://genome.ucsc.edu/goldenPath/help/wiggle.html).

okay important: this option can only be used with individual phylogenetic models — not with sets of models and a (nontrivial) HMM. so don't try it, it's not giving what you want 💀

• --window-wig, -W <size> — (can be used instead of -g or -y) like --window but it outputs scores in fixed-step WIG format, as with --base-by-base. scores for the positive strand only are output. 🌈
• --msa-format, -i <type> — input format for the alignment. may be FASTA, PHYLIP, MPM, SS, or MAF (default is to guess the format from the file contents — it just knows 🔮).
• --refidx, -r <ref_seq> — index of the reference sequence for coordinates. use 0 to indicate the coordinate system of the alignment as a whole. default is 1, for the first sequence. ⭐
• --output-bed, -d — (for use with -g) generate output in bed format rather than GFF. 🛏️✨
• --verbose, -v — verbose mode. print messages to stderr describing what the program is doing. it's basically the program narrating its own life 💬
• --help, -h — print this help message. 🫶

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okay that's the whole page bestie, you ate it 🎀 this manual was serving phastOdds version 1.4, dated May 2016 — so like, vintage, but make it slay. bye bye, go score something 🔥💖🦋