MVIEW 1.41.10 a multiple alignment viewer alignment:multiple display N. P. Brown Brown, N.P., Leroy C., Sander C. (1998). MView: A Web compatible database search or multiple alignment viewer. Bioinformatics. 14(4):380-381. mview_alig mview_alig perl "mview" 0 alig Alignment File perl " $value" 1000 readseq_ok_alig perl 1 in Type of alignment (-in) perl ($value eq "phylip")? " -in msf " : " -in $value" clustal 2 pearson msf clustal phylip hssp plain multas mips from_phylip perl "fmtseq -p -f17 $alig > $alig.tmp; mv $alig.tmp $alig; " -10 perl $in eq "phylip" main_formatting_options Main formatting options 2 ruler Attach a ruler (-ruler) perl ($value)? " -ruler on":"" 2 alignment Show alignment (-alignment) perl ($value)? " " : " -alignment off" 1 2 consensus Show consensus (-consensus) perl ($value)? " -consensus on":"" 2 dna Use DNA/RNA colormaps and/or consensus groups (-dna) perl ($value)? " -dna":"" 0 2 alignment_options Alignment options 3 coloring Colour scheme (-coloring) perl ($value)? " -coloring $value":"" 3 any consensus group identity none -coloring consensus: will colour only those residues that belong to a specified physicochemical class that is conserved in at least a specified percentage of all rows for a given column. This defaults to 70% and and may be set to another threshold, eg., -coloring consensus -threshold 80 would specify 80%. Note that the physicochemical classes in question can be confined to individual residues. -coloring group, is like -coloring consensus, but colours residues by the colour of the class to which they belong. By default, the consensus computation counts gap characters, so that sections of the alignment may be uncolored where the presence of gaps prevents the non-gap count from reaching the threshold. Setting -con_gaps off prevents this, allowing sequence-only based consensus thresholding. The default palette assumes the input alignment is of protein sequences and sets their colours according to amino acid physicochemical properties: another palette should be selected for DNA or RNA alignments. Consensus colouring is complicated and some understanding of palettes and consensus patterns is required first before trying to explain alignment consensus colouring. threshold Threshold percentage for consensus coloring (-threshold) perl (defined $value && $value != $vdef)? " -threshold $value":"" 70.0 3 ignore Ignore singleton or class group (-ignore) perl ($value && $value ne $vdef)? " -ignore $value" : "" none 3 class none singleton Tip: If you want to see only the conserved residues above the threshold (ie., only one type of conserved residue per column), add the option -ignore class. consensus_options Consensus options perl $consensus 3 con_coloring Basic style of coloring (-con_coloring) perl ($value)? " -con_coloring $value":"" 3 any identity none -coloring consensus: will colour only those residues that belong to a specified physicochemical class that is conserved in at least a specified percentage of all rows for a given column. This defaults to 70% and and may be set to another threshold, eg., -coloring consensus -threshold 80 would specify 80%. Note that the physicochemical classes in question can be confined to individual residues. -coloring group, is like -coloring consensus, but colours residues by the colour of the class to which they belong. By default, the consensus computation counts gap characters, so that sections of the alignment may be uncolored where the presence of gaps prevents the non-gap count from reaching the threshold. Setting -con_gaps off prevents this, allowing sequence-only based consensus thresholding. The default palette assumes the input alignment is of protein sequences and sets their colours according to amino acid physicochemical properties: another palette should be selected for DNA or RNA alignments. Consensus colouring is complicated and some understanding of palettes and consensus patterns is required first before trying to explain alignment consensus colouring. perl $consensus con_threshold Consensus line thresholds (in range 50..100) (separated by commas) (-con_threshold) perl ($value && $value ne $vdef)? " -con_threshold $value":"" 100,90,80,70 3 perl $consensus 50 con_ignore Ignore singleton or class group (-con_ignore) perl ($value && $value ne $vdef)? " -con_ignore $value" : "" none 3 class none singleton perl $consensus hybrid_alignment_consensus_options Hybrid alignment and consensus options 3 con_gaps Count gaps during consensus computations (-con_gaps) perl ($value)? "" : " -con_gaps off" 1 3 general_row_column_filters General row/column filters 3 top Report top N hits (-top) perl (defined $value)? " -top $value":"" 3 range Display column range M..N as numbered by ruler (M,N) (-range) perl ($value && ($value =~ s/,/:/g))? " -range $value":"" 3 maxident Only report sequences with %identity <= N (-maxident) perl (defined $value && $value != $vdef)? " -maxident $value":"" 100 3 ref Use row N or row identifier as %id entity reference (-ref) perl ($value)? " -ref $value":"" 3 keep_only Keep only the rows from start to end (separated by commas: start,end) (-keep) perl ($value && ($value =~ s/,/../))? " -disc \\"/.*/\\" -keep $value" : "" 3 disc Discard rows from start to end (separated by commas: start,end) (-disc) perl ($value && ($value =~ s/,/../))? " -disc $value" : "" 3 nops Display rows unprocessed (separated by commas) (-nops) perl ($value)? " -nops $value" : "" 3 general_formatting_options General formatting options 3 width Paginate in N columns of alignment (-width) perl (defined $value)? " -width $value":"" 3 gap Use this character as the gap (-gap) perl ($value)? " -gap $value" : " " 3 label0 Switch off label: row number (-label0) perl ($value)? " -label0":"" 3 label1 Switch off label: identifier (-label1) perl ($value)? " -label1":"" 3 label2 Switch off label: description (-label2) perl ($value)? " -label2":"" 3 label3 Switch off label: scores (-label3) perl ($value)? " -label3":"" 3 label4 Switch off label: percent identity (-label4) perl ($value)? " -label4":"" 3 html_markup_options HTML markup options 3 html_output HTML output perl " -html $value" full 1 full head body data css off perl $_html && $out eq "html" pagecolor Page backgound color (-pagecolor) perl ($value)? " -pagecolor $value" : "" 3 20 textcolor Page text color (-textcolor) perl ($value && $value ne $vdef)? " -textcolor $value" : "" black 3 20 linkcolor Link color (-linkcolor) perl ($value && $value ne $vdef)? " -linkcolor $value" : "" blue 3 20 alinkcolor Active link color (-alinkcolor) perl ($value && $value ne $vdef)? " -alinkcolor $value" : "" red 3 20 vlinkcolor Visited link color (-vlinkcolor) perl ($value && $value ne $vdef)? " -vlinkcolor $value" : "" purple 3 20 alncolor Alignment background color (-alncolor) perl ($value)? " -alncolor $value" : "" 3 20 symcolor Alignment default text color (-symcolor) perl ($value)? " -symcolor $value" : " " 3 20 gapcolor Alignment gap color (-gapcolor) perl ($value)? " -gapcolor $value" : "" 3 20 bold Use bold emphasis for coloured residues (-bold) perl ($value)? " -bold":"" 3 css Use Cascading Style Sheets (-css) perl ($value eq "on")? " -css on" : "" off 3 off on html_output_file perl " > mview.html" 2000 perl $_html && $out eq "html" html_file perl $_html && $out eq "html" mview.html alig_file perl $out eq "msf" || $out eq "pearson" || $out eq "pir" mview*.out readseq_ok_alig perl 1 out Output format (-out) perl ($value eq "html")? "" : " -out $value" html 1 html msf pearson pir rdb