# HG changeset patch # User dcorreia # Date 1485441287 18000 # Node ID c7be0bcf3f1036c50f804516e2ea62d29603292d Uploaded diff -r 000000000000 -r c7be0bcf3f10 clustalo.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clustalo.xml Thu Jan 26 09:34:47 2017 -0500 @@ -0,0 +1,220 @@ + + Multiple sequence alignment software + + operation_0499 + operation_0492 + + + clustalo + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + getTree == "--guidetree-out=guidetree.txt" + + + + + + + + + + + + + + + + + Multiple sequence input file (- for stdin) + --hmm-in= HMM input files + --dealign Dealign input sequences + --profile1, --p1= Pre-aligned multiple sequence file (aligned columns will be kept fix) + --profile2, --p2= Pre-aligned multiple sequence file (aligned columns will be kept fix) + --is-profile Disable check if profile, force profile (default no) + -t, --seqtype *Protein, RNA, DNA* Force a sequence type (default: auto) + --infmt *fa[sta], clu[stal], msf, phy[lip], selex, st[ockholm], vie[nna]*. Forced sequence input file format (default: auto) + +----- + +Clustering: + --distmat-in= Pairwise distance matrix input file (skips distance computation) + --distmat-out= Pairwise distance matrix output file + --guidetree-in= Guide tree input file (skips distance computation and guide-tree clustering step) + --guidetree-out= Guide tree output file + --pileup Sequentially align sequences + --full Use full distance matrix for guide-tree calculation (might be slow; mBed is default) + --full-iter Use full distance matrix for guide-tree calculation during iteration (might be slowish; mBed is default) + --cluster-size= soft maximum of sequences in sub-clusters + --clustering-out= Clustering output file + --trans= Use transitivity (default: 0) + --posterior-out= Posterior probability output file + --use-kimura Use Kimura distance correction for aligned sequences (default no) + --percent-id convert distances into percent identities (default no) + +---- + +Alignment Output: + -o, --outfile= Multiple sequence alignment output file (default: stdout) + --outfmt *fa[sta], clu[stal], msf, phy[lip], selex, st[ockholm], vie[nna]* MSA output file format (default: fasta) + --residuenumber, --resno in Clustal format print residue numbers (default no) + --wrap= number of residues before line-wrap in output + --output-order *input-order, tree-order* MSA output order like in input/guide-tree + +---- + +Iteration: + --iterations, --iter= Number of (combined guide-tree/HMM) iterations + --max-guidetree-iterations= Maximum number of guidetree iterations + --max-hmm-iterations= Maximum number of HMM iterations + +---- + +Limits (will exit early, if exceeded): + --maxnumseq= Maximum allowed number of sequences + --maxseqlen= Maximum allowed sequence length + +---- + +Miscellaneous: + --auto Set options automatically (might overwrite some of your options) + --threads= Number of processors to use + --pseudo= Input file for pseudo-count parameters + -l, --log= Log all non-essential output to this file + -h, --help Print this help and exit + -v, --verbose Verbose output (increases if given multiple times) + --version Print version information and exit + --long-version Print long version information and exit + --force Force file overwriting + ]]> + + + 10.1038/msb.2011.75 + +