esl-alimanip(1)

📦
version 3.3.2 · 2 versions
, in fedora 43, fedora 44

💖 esl-alimanip — it's giving "alignment glow-up" ✨

okay bestie, welcome to esl-alimanip(1) from the Easel manual 💅 this lil icon is here to manipulate a multiple sequence alignment, and honestly? it eats.

🌸 SYNOPSIS 🌸

esl-alimanip [options] msafile

🦋 DESCRIPTION 🦋

so like, esl-alimanip can manipulate the multiple sequence alignment(s) in msafile in various ways — no cap. Options exist to remove specific sequences, reorder sequences, designate reference columns using Stockholm "#=GC RF" markup, and add annotation that numbers columns. it's a whole vibe.

The alignments can be of protein or DNA/RNA sequences. All alignments in the same msafile must be either protein or DNA/RNA. The alphabet will be autodetected unless one of the options --amino, --dna, or --rna are given. she's smart like that 💅

✨ OPTIONS ✨

  • -h — Print brief help; includes version number and summary of all options, including expert options. the lil "hey what's up" of flags 🫶
  • -o <f> — Save the resulting, modified alignment in Stockholm format to a file <f>. The default is to write it to standard output. so if you don't say anything, she's yelling into the void (stdout) 📢
  • --informat <s> — Assert that msafile is in alignment format <s>, bypassing format autodetection. Common choices for <s> include: stockholm, a2m, afa, psiblast, clustal, phylip. For more information, and for codes for some less common formats, see main documentation. The string <s> is case-insensitive (a2m or A2M both work). she does NOT care about your caps lock era 🔠
  • --outformat <s> — Write the output in alignment format <s>. Common choices for <s> include: stockholm, a2m, afa, psiblast, clustal, phylip. The string <s> is case-insensitive (a2m or A2M both work). Default is stockholm. the main character format, as always 👑
  • --devhelp — Print help, as with -h, but also include undocumented developer options. These options are not listed below, are under development or experimental, and are not guaranteed to even work correctly. Use developer options at your own risk. The only resources for understanding what they actually do are the brief one-line description printed when --devhelp is enabled, and the source code. it's giving "trust me bro" energy fr fr 💀

🔥 EXPERT OPTIONS 🔥

  • --lnfract <x> — Remove any sequences with length less than <x> fraction the length of the median length sequence in the alignment. bye shorties 👋
  • --lxfract <x> — Remove any sequences with length more than <x> fraction the length of the median length sequence in the alignment. bye long-winded besties 👋
  • --lmin <n> — Remove any sequences with length less than <n> residues. too tiny, not iconic 🎀
  • --lmax <n> — Remove any sequences with length more than <n> residues. too extra, dial it back 💅
  • --rfnfract <x> — Remove any sequences with nongap RF length less than <x> fraction the nongap RF length of the alignment. RF stands for reference, iykyk ✨
  • --detrunc <n> — Remove any sequences that have all gaps in the first <n> non-gap #=GC RF columns or the last <n> non-gap #=GC RF columns. gap city = eviction notice 🚪
  • --xambig <n> — Remove any sequences that has more than <n> ambiguous (degenerate) residues. ambiguous queenies get the boot 😭
  • --seq-r <f> — Remove any sequences with names listed in file <f>. Sequence names listed in <f> can be separated by tabs, new lines, or spaces. The file must be in Stockholm format for this option to work. block list, but make it bioinformatics 📝
  • --seq-k <f> — Keep only sequences with names listed in file <f>. Sequence names listed in <f> can be separated by tabs, new lines, or spaces. By default, the kept sequences will remain in the original order they appeared in msafile, but the order from <f> will be used if the --k-reorder option is enabled. The file must be in Stockholm format for this option to work. the VIP list 💖
  • --small — With --seq-k or --seq-r, operate in small memory mode. The alignment(s) will not be stored in memory, thus --seq-k and --seq-r will be able to work on very large alignments regardless of the amount of available RAM. The alignment file must be in Pfam format and --informat pfam and one of --amino, --dna, or --rna must be given as well. low RAM? no problem, she adapts 🧚
  • --k-reorder — With --seq-k <f>, reorder the kept sequences in the output alignment to the order from the list file <f>. your order, your rules 👑
  • --seq-ins <n> — Keep only sequences that have at least 1 inserted residue after nongap RF position <n>. insertions = relevance, apparently ✨
  • --seq-ni <n> — With --seq-ins require at least <n> inserted residues in a sequence for it to be kept. minimum effort required, bestie 💪
  • --seq-xi <n> — With --seq-ins allow at most <n> inserted residues in a sequence for it to be kept. maximum chaos tolerated 🚧
  • --trim <f> — File <f> is an unaligned FASTA file containing truncated versions of each sequence in the msafile. Trim the sequences in the alignment to match their truncated versions in <f>. If the alignment output format is Stockholm (the default output format), all per-column (GC) and per-residue (GR) annotation will be removed from the alignment when --trim is used. However, if --t-keeprf is also used, the reference annotation (GC RF) will be kept. a haircut, basically ✂️
  • --t-keeprf — Specify that the 'trimmed' alignment maintain the original reference (GC RF) annotation. Only works in combination with --trim. keep the RF, lose the rest 💜
  • --minpp <x> — Replace all residues in the alignments for which the posterior probability annotation (#=GR PP) is less than <x> with gaps. The PP annotation for these residues is also converted to gaps. <x> must be greater than 0.0 and less than or equal to 0.95. not confident? gap. periodt 💀
  • --tree <f> — Reorder sequences by tree order. Perform single linkage clustering on the sequences in the alignment based on sequence identity given the alignment to define a 'tree' of the sequences. The sequences in the alignment are reordered according to the tree, which groups similar sequences together. The tree is output in Newick format to <f>. family tree but for sequences 🌳
  • --reorder <f> — Reorder sequences to the order listed in file <f>. Each sequence in the alignment must be listed in <f>. Use --k-reorder to reorder only a subset of sequences to a subset alignment file. The file must be in Stockholm format for this option to work. everyone's invited, no skipping 📋
  • --mask2rf <f> — Read in the 'mask' file <f> and use it to define new #=GC RF annotation for the alignment. <f> must be a single line, with exactly <alen> or <rflen> characters, either the full alignment length or the number of nongap #=GC RF characters, respectively. Each character must be either a '1' or a '0'. The new #=GC RF markup will contain an 'x' for each column that is a '1' in lane mask file, and a '.' for each column that is a '0'. If the mask is of length <rflen> then it is interpreted as applying to only nongap RF characters in the existing RF annotation, all gap RF characters will remain gaps and nongap RF characters will be redefined as above. ones and zeros doing the absolute most 🎭
  • --m-keeprf — With --mask2rf, do not overwrite existing nongap RF characters that are included by the input mask as 'x', leave them as the character they are. if it's already slaying, don't touch it 💅
  • --num-all — Add annotation to the alignment numbering all of the columns in the alignment. count every single one, bestie 🔢
  • --num-rf — Add annotation to the alignment numbering the non-gap (non '.') #=GC RF columns of the alignment. only the non-gap girlies get numbers ✨
  • --rm-gc <s> — Remove certain types of #=GC annotation from the alignment. <s> must be one of: RF, SS_cons, SA_cons, PP_cons. choose wisely 🗑️
  • --sindi — Annotate individual secondary structures for each sequence by imposing the consensus secondary structure defined by the #=GC SS_cons annotation. matching fits, one structure at a time 🎀
  • --post2pp — Update Infernal's cmalign 0.72-1.0.2 posterior probability "POST" annotation to "PP" annotation, which is read by other miniapps, including esl-alimask and esl-alistat. glow-up from legacy naming 🦋
  • --amino — Assert that the msafile contains protein sequences. protein era 🥩
  • --dna — Assert that the msafile contains DNA sequences. double helix era 🧬
  • --rna — Assert that the msafile contains RNA sequences. single strand era 🌀

💜 SEE ALSO 💜

Copyright (C) 2020 Howard Hughes Medical Institute.

Freely distributed under the BSD open source license. iconic, generous, legally clear 💖

👑 AUTHOR 👑

and that's the whole page bestie!! go forth and manipulate those alignments responsibly 🌈✨

Easel 0.48 — Nov 2020 — and this esl-alimanip(1) page is officially done, mwah 💋🫶

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