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
