DATASET_ALIGNMENT #visualize multiple sequence alignments directly on the tree. Alignment must be in FASTA format. #lines starting with a hash are comments and ignored during parsing #=================================================================# # MANDATORY SETTINGS # #=================================================================# #select the separator which is used to delimit the data below (TAB,SPACE or COMMA).This separator must be used throughout this file. #SEPARATOR TAB #SEPARATOR SPACE SEPARATOR COMMA #label is used in the legend table (can be changed later) DATASET_LABEL,example alignment #dataset color (can be changed later) COLOR,#ff0000 #=================================================================# # OPTIONAL SETTINGS # #=================================================================# #define one or more custom alignment coloring schemes. They will appear in the color scheme selection box #first field defines the scheme name, followed by a list of letters and their color assignments. Letters which do not #have a color defined will be displayed with a white background CUSTOM_COLOR_SCHEME,MY_SCHEME_1,A=#d2d0c9,M=#d2d0c9,I=#d2d0c9,L=#d2d0c9,V=#d2d0c9,P=#746f69,G=#746f69,C=#746f69,F=#d0ad16,Y=#d0ad16,W=#d0ad16,S=#34acfb,T=#34acfb,N=#34acfb,Q=#34acfb,R=#34fb54,K=#34fb54,H=#34fb54,D=#fb4034,E=#fb4034 CUSTOM_COLOR_SCHEME,MY_SCHEME_2,A=#30a040,R=#2015a5,N=#10ffa0,D=#6048c0,C=#608a80,Q=#601f00,E=#5048c0,G=#702048,H=#a5a4a4,I=#1a30f0,L=#11a0f0,K=#003505,M=#00a0f0,F=#10a0f0,P=#0ff300,S=#93f300,T=#33ff00,W=#0a30f0,Y=#25a4a4,V=#90a3f0 #When dotted highlights are set to 'reference', list of reference leaf nodes specified in HIGHLIGH_REFERENCES field will be used when creating the highlights. #You can specify one or more references. When multiple reference sequences are used, sequences are compared to the first reference above them in the alignment. In this case, the top #leaf should be one of the references as well. #HIGHLIGHT_REFERENCES,reference_leaf1,reference_leaf2... #=================================================================# # all other optional settings can be set or changed later # # in the web interface (under 'Datasets' tab) # #=================================================================# #left margin, used to increase/decrease the spacing to the next dataset. Can be negative, causing datasets to overlap. Used only for text labels which are displayed on the outside MARGIN,0 #font size factor; default font size will be slightly less than the available space between leaves, but you can set a multiplication factor here to increase/decrease it (values from 0 to 1 will decrease it, values above 1 will increase it) SIZE_FACTOR,1 #color scheme to use; possible values are 'none','clustal','zappo','taylor','hphob','helix','strand','turn' and 'buried' #if CUSTOM_COLOR_SCHEME is defined, its label can also be used here COLOR_SCHEME,clustal #start and stop residue of the alignment to display; note that the complete length should be below ~4000 residues START_POSITION,1 END_POSITION,100 #highlight residues in each column by comparing them to the consensus or a reference sequence (specified above in the HIGHLIGHT_REFERENCES field). Non-highlighted residues are displayed as dots. #possible values are 'none', 'consensus' and 'reference' #HIGHLIGHT_TYPE,none #When HIGHLIGHT_TYPE is not 'none', matching residues are highlighted by default. To highlight non-matching residues instead, set this to 1 #HIGHLIGHT_DISAGREEMENTS,0 #when HIGHLIGHT_TYPE is not set to 'none', backgrounds of each dot will be colored based on the underlying residue if COLORED_DOTS is set to 1 #COLORED_DOTS,1 #if any reference sequences are defined in the HIGHLIGHT_REFERENCES field, these can be highlighted in the alignment with a box drawn around them #MARK_REFERENCES,1 #when MARK_REFERENCES is set to 1, these fields define the style of the box #REFERENCE_BOX_BORDER_WIDTH,1 #REFERENCE_BOX_BORDER_COLOR,#ff000 #REFERENCE_BOX_FILL_COLOR,#aaaaaa #inverse the color of gap fields to make them stand out #INVERSE_GAPS,0 #display the consensus sequence below the alignment DISPLAY_CONSENSUS,1 #when calculating the consensus sequence, top residue whose percentage is above this threshold will be included in the consensus CONSENSUS_THRESHOLD,50 #when calculating the consensus sequence, ignore gaps in the alignment #IGNORE_GAPS,1 #display the residue conservation graph below the alignment DISPLAY_CONSERVATION,1 #display conservation graph bars in color (green for >95%, orange for >30% and red for <30%) #COLOR_GRAPH,1 #=================================================================# # Put the actual alignment below the "DATA" keyword # #=================================================================# #alignment must be in FASTA format #lines starting with a ">" sign should contain the sequence IDs (exactly matching the tree leaf IDs) #all lines until the next sequence ID line will be taken as the actual aligned sequence string #all space characters will be removed automatically #empty lines are ignored DATA #Example alignment >SRC_AVIS2 EEWYFGKI-- ---TRRESER LLLNP----- -----ENPRG TFLVRESET- ---------- ---------- ---------- ------TKGA YCLSVSDFDN ---------- ---------- ---------- ---------- ---------- --AKGLNVKH YKIRKLDS-- ---------- -----GGFYI TS-------- ----RTQFSS --LQQLVAYY SKHADG >FGR_HUMAN EEWYFGKI-- ---GRKDAER QLLSP----- -----GNPQG AFLIRESET- ---------- ---------- ---------- ------TKGA YSLSIRDWDQ ---------- ---------- ---------- ---------- ---------- --TRGDHVKH YKIRKLDM-- ---------- -----GGYYI TT-------- ----RVQFNS --VQELVQHY MEVNDG >Q94879 EPWYFRKI-- ---KRIEAEK KLLLP----- -----ENEHG AFLIRDSES- ---------- ---------- ---------- ------RHND YSLSVRDG-- ---------- ---------- ---------- ---------- ---------- -----DTVKH YRIRQLDE-- ---------- -----GGFFI AR-------- ----RTTFRT --LQELVEHY SKDSDG