DLESS(1)

🌸 DLESS 🌸

okay bestie, welcome to dless(1) — it's a User Commands page and it's lowkey iconic, let's get into it 💅

✨ NAME ✨

dless — attempts to identify elements under selection in all species or in

yes girl, the original sentence just ends like that, no cap. we move. 🫶

🦋 DESCRIPTION 🦋

So what does this thing even do?? It attempts to identify elements under selection in all species, or in some subset of species, based on a multiple alignment and a phylo-HMM. ✨

More specifically, it detects elements that:

• have been under selection since the divergence of all species in the given set,
• were "born" on some branch of the tree since their divergence and have been under selection since, or
• were present in the common ancestor but "died" (ceased to be under selection) on some branch of the tree.

Currently it only detects negative selection, but extensions to detect positive selection as well are planned. 🔮

💜 EXAMPLE 💜

(this section is literally empty in the original, so… vibe check passed, nothing to see, moving on 🙈)

🎀 OPTIONS 🎀

• --rho, -R <rho> — default 0.3. that's it, that's the whole description, she's mysterious like that 💀
• --transitions, -t [~]<mu>,<nu> — sets the transition probabilities of the two-state HMM using the values of <mu> and <nu> you give it (both gotta be between 0 and 1).
• --phi, -p [~]<phi> — default 0.5. again, no further notes. she's giving minimalism ✨
• --target-coverage, -C [~]<gamma> — alternative to transitions, use it with --expected-length. Sets the transition parameters so that the expected fraction of sites in conserved elements is <gamma> (between 0 and 1). Heads up: this is a prior rather than posterior expectation, and it assumes stationarity of the state-transition process. This option causes the ratio mu/nu to be fixed at (1-gamma)/gamma, and together with --expected-length, completely defines the transition probabilities. math queen behavior 👑
• --expected-length, -E [~]<omega> — alternative to --transitions, use it with --target-coverage. Sets transition probabilities such that the (prior) expected length of a conserved element is <omega>. The parameter mu is set to 1/omega. slay 🫶
• --msa-format, -i FASTA|PHYLIP|MPM|MAF|SS — the alignment format. Default is to guess the format from the file contents. ngl, the program msa_view can be used for conversion if you need it. 🔥
• --refseq, -M <fname> — for use with --msa-format MAF. Reads the complete text of the reference sequence from <fname> (FASTA format) and combines it with the contents of the MAF file to produce a complete, ordered representation of the alignment. The reference sequence of the MAF file is assumed to be the one that appears first in each block. 📖
• --refidx, -r <refseq_idx> — use the coordinate frame of the specified sequence in the output. The default value is 1, the first sequence in the alignment; 0 indicates the coordinate frame of the entire multiple alignment. 🧭
• --seqname, -N <name> — use the specified string for the 'seqname' (GFF) or 'chrom' field in the output file. The default is obtained from the input file name (double filename root, e.g., "chr22" if the input file is "chr22.35.ss"). 💖
• --idpref, -P <name> — use the specified string as the prefix of generated ids in the output file. Can be used to ensure the ids are unique. The default is obtained from the input file name (single filename root, e.g., "chr22.35" if the input file is "chr22.35.ss"). 🎀
• --indel-model, -I alpha,beta,tau[,alpha2,beta2,tau2] — uses a simple model of insertions and deletions that assumes a known indel history and at most one indel per branch of the tree at any given position. The parameters alpha and beta are rates of insertion and deletion, respectively, per expected substitution per site, and the parameter tau is approximately the inverse of the expected indel length (see indelFit). If two sets of parameters are given, the first will be used for nonconserved regions and the second for conserved regions. If --indel-history is not used, a history will be inferred on the fly using a simple parsimony algorithm. 🧚
• --indel-history, -H <file.ih> — for use with --indel-model. Uses the specified indel history (see indelHistory). 🌈
• --help, -h — shows this help message and exits. the classic. we love her. 😌

okay that's the whole page bestie, and for the cute sign-off: this is dless version 1.4, dated May 2016 💖 — yeah she's vintage, she's an elder, and she still ate. periodt. 👑