About InSites

InSites, developed by Wenjie Deng and Jim Mullins at University of Washington, is a web interface to detect phylogenetically informative sites among a set of aligned nucleotide or amino acid sequences. An informative site is defined as a site where two or more sequences share the same base (or residue) that is different from a reference sequence. The sequence alignment must include this reference sequence. InSites can detect two types of informative sites:

1. Informative sites are based on a complete set of aligned sequences
2. Informative sites are based on a group of sequences where the same difference occurs in at least 2 sequences, as compared to the reference sequence. This requires that the user provide a "group file" indicating group membership of each sequence.

• Alignment file: A nexus or phylip file in sequential format with the reference (here using a consensus) sequence must be listed first in the alignment. The sequence name must NOT contain any blank spaces.

Example of nexus file:

#NEXUS 

BEGIN DATA;
	DIMENSIONS  NTAX=11 NCHAR=100;
	FORMAT DATATYPE=DNA  MISSING=? GAP=- ;
MATRIX
[                       10        20        30        40        50        60        70        80        90        100
[                       .         .         .         .         .         .         .         .         .         .  

Consensus      ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTAGATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGAAACACC  [100]
Dec03_1        ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTATATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGCAACACC  [100]
Dec03_2        ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTATATACATGGGAGAAAATTAGGTTAAGGCCAGGGGGAAAGCAAACTTATAGGATGAAACACC  [100]
Dec03_3        ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTAGATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGAAACACC  [100]
Dec03_4        ATGGGTGGGAGAGCATCAATATTAAGAGGGGGAAAATTAGATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGAAACACC  [100]
Dec03_5        ATGGGTGGGAGAGCATCAATATTAAGAGGGGGAAAATTAGATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGAAACACC  [100]
Mar04_1        ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTATATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGCAACACC  [100]
Mar04_2        ATGGGTGGGAGAGCGTCAATATTAAGAGGCTTAAAATTAGATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGAAACACC  [100]
Mar04_7        ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTAGATACATGGGAGAAAATTAGGTTAAGGCCAGGGGGAAAGCAAACTTATAGGATGAAACGCC  [100]
Mar04_8        ATGGATGCGAGAGCGTCAATATTAAGAGGGGGAAAATTAGATACATGGGGGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGAAACACC  [100]
Mar04_9        ATGGGTGCGAGAGCGTCAATATTAAGAGGGTTAAAATTAGATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGAAACACC  [100]
;
END;

Example of phylip file:

11 100
Consensus      ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTAGATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGAAACACC
Dec03_1        ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTATATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGCAACACC
Dec03_2        ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTATATACATGGGAGAAAATTAGGTTAAGGCCAGGGGGAAAGCAAACTTATAGGATGAAACACC
Dec03_3        ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTAGATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGAAACACC
Dec03_4        ATGGGTGGGAGAGCATCAATATTAAGAGGGGGAAAATTAGATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGAAACACC
Dec03_5        ATGGGTGGGAGAGCATCAATATTAAGAGGGGGAAAATTAGATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGAAACACC
Mar04_1        ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTATATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGCAACACC
Mar04_2        ATGGGTGGGAGAGCGTCAATATTAAGAGGCTTAAAATTAGATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGAAACACC
Mar04_7        ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTAGATACATGGGAGAAAATTAGGTTAAGGCCAGGGGGAAAGCAAACTTATAGGATGAAACGCC
Mar04_8        ATGGATGCGAGAGCGTCAATATTAAGAGGGGGAAAATTAGATACATGGGGGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGAAACACC
Mar04_9        ATGGGTGCGAGAGCGTCAATATTAAGAGGGTTAAAATTAGATACATGGGAGAGAATTAGGTTAAGGCCAGGGGGAAAGAAAACTTATAGGATGAAACACC

• Group file (optional): A tab-delimited file with two columns in which the first column defines a group name and the second column lists a sequence name belonging to that group. For example, groups could be sequences derived from different sample time-points or tissues/compartments.

Example of a group file defining two groups based on sampling data of 10 sequences:

Dec03	Dec03_1
Dec03	Dec03_2
Dec03	Dec03_3
Dec03	Dec03_4
Dec03	Dec03_5
Mar04	Mar04_1
Mar04	Mar04_2
Mar04	Mar04_7
Mar04	Mar04_8
Mar04	Mar04_9

• Aligned informative sites: An output file where all detected informative sites are aligned.

Example of aligned informative sites:

                1334579
               85120394

Consensus      CGGGGGAA
Dec03_1        ....T..C
Dec03_2        ....TAC.
Dec03_3        ........
Dec03_4        GA......
Dec03_5        GA......
Mar04_1        ....T..C
Mar04_2        G.TT....
Mar04_7        .....AC.
Mar04_8        ........
Mar04_9        ..TT....

• Tab-delimited informative sites & summary: A tab-delimited output file containing all detected informative sites and summarizing all informative and private sites.

Example of tab-delimited informative sites & summary:

		8	15	31	32	40	53	79	94	Total_informative	Total_private	private_site(na/aa)
Consensus	C	G	G	G	G	G	A	A		0			0	
Dec03_1		.	.	.	.	T	.	.	C		2			0	
Dec03_2		.	.	.	.	T	A	C	.		3			0	
Dec03_3		.	.	.	.	.	.	.	.		0			0	
Dec03_4		G	A	.	.	.	.	.	.		2			0	
Dec03_5		G	A	.	.	.	.	.	.		2			0	
Mar04_1		.	.	.	.	T	.	.	C		2			0	
Mar04_2		G	.	T	T	.	.	.	.		3			1	30(C)
Mar04_7		.	.	.	.	.	A	C	.		2			1	98(G)
Mar04_8		.	.	.	.	.	.	.	.		0			2	5(A),50(G)
Mar04_9		.	.	T	T	.	.	.	.		2			0	

A		0	2	0	0	0	2	8	8
C		7	0	0	0	0	0	2	2
G		3	8	8	8	7	8	0	0
T		0	0	2	2	3	0	0	0
Total		10	10	10	10	10	10	10	10

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