The input sequence file is an alignment of nucleotide or amino-acid sequences. We accept three types of sequence files, which are fasta, nexus or phylip. The sequence data set could be in either sequential or interleaved format. The name of sequences MUST NOT contain any whitespace characters (tab or space). It is recommended that the sequence name is comprised of alphabetical characters, digits or underscore. The program will replace any other characters with underscore "_".
Example of Nexus file in sequential format:
#NEXUS BEGIN DATA; DIMENSIONS NTAX=12 NCHAR=150; FORMAT DATATYPE=DNA MISSING=? GAP=- ; MATRIX 092398_316 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 092398_339 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 092398_315 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 092398_317 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 092398_312 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 082599_889 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACTCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 082599_894 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCCAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACGACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 082599_896 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 082599_916 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 082599_917 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT ML1365_1 GAAGAAGAGGTAATAATTAGATCACAAAATTTCACAGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT ML1365_2 GAAGAAGAGGTAATAATTAGATCACAAAATTTCACAGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT ; END;
Example of Nexus file in interleaved format:
#NEXUS BEGIN DATA; DIMENSIONS NTAX=12 NCHAR=150; FORMAT DATATYPE=DNA MISSING=? GAP=- INTERLEAVE ; MATRIX 092398_316 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 092398_339 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 092398_315 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 092398_317 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 092398_312 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 082599_889 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 082599_894 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCCAAAACCATATTAGTACAGCTGAATGAAACTGTACA 082599_896 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 082599_916 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 082599_917 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA ML1365_1 GAAGAAGAGGTAATAATTAGATCACAAAATTTCACAGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA ML1365_2 GAAGAAGAGGTAATAATTAGATCACAAAATTTCACAGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 092398_316 AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 092398_339 AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 092398_315 AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 092398_317 AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 092398_312 AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 082599_889 AATTAATTGTACAAGACTCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 082599_894 AATTAATTGTACAAGACCCAACGACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 082599_896 AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 082599_916 AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 082599_917 AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT ML1365_1 AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT ML1365_2 AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT ; END;
Example of phylip file in sequential format:
12 150 092398_316 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 092398_339 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 092398_315 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 092398_317 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 092398_312 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 082599_889 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACTCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 082599_894 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCCAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACGACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 082599_896 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 082599_916 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT 082599_917 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT ML1365_1 GAAGAAGAGGTAATAATTAGATCACAAAATTTCACAGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT ML1365_2 GAAGAAGAGGTAATAATTAGATCACAAAATTTCACAGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT
Example of phylip file in interleaved format:
12 150 092398_316 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 092398_339 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 092398_315 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 092398_317 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 092398_312 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 082599_889 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 082599_894 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCCAAAACCATATTAGTACAGCTGAATGAAACTGTACA 082599_896 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 082599_916 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA 082599_917 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA ML1365_1 GAAGAAGAGGTAATAATTAGATCACAAAATTTCACAGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA ML1365_2 GAAGAAGAGGTAATAATTAGATCACAAAATTTCACAGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT AATTAATTGTACAAGACTCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT AATTAATTGTACAAGACCCAACGACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT
Example of fasta file:
>092398_316 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT >092398_339 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT >092398_315 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT >092398_317 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT >092398_312 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT >082599_889 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA AATTAATTGTACAAGACTCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT >082599_894 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCCAAAACCATATTAGTACAGCTGAATGAAACTGTACA AATTAATTGTACAAGACCCAACGACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT >082599_896 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT >082599_916 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT >082599_917 GAAGAAGAGGTAATAATTAGATCACAGAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT >ML1365_1 GAAGAAGAGGTAATAATTAGATCACAAAATTTCACAGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT >ML1365_2 GAAGAAGAGGTAATAATTAGATCACAAAATTTCACAGACAATGCTAAAACCATATTAGTACAGCTGAATGAAACTGTACA AATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGCATACATATAGCACCAGGGAGAGCATTTTAT
DNA or amino-acid. You must select correct data type for your sequence alignment file.
A text file contains a list of outgroup sequence name(s) which must match the sequence name(s) in sequence file. It must be one sequence name per line. If user provides outgroup file, DIVER will calculate the Most Recent Common Ancestor (MRCA) and divergence from the MRCA.
Example:
ML1365_1 ML1365_2
A text file contains two tab delimited columns (1) a list of group names and (2) the corresponding sequence names which must match the sequence names in sequence file. For example, groups could be different sample time points or tissues/compartments. If user provides a group file, DIVER will calculate diversity for each defined group. Otherwise, diversity among all sequences will be calculated as a default group.
Example:
092398 092398_316 092398 092398_339 092398 092398_315 092398 092398_317 092398 092398_312 082599 082599_889 082599 082599_894 082599 082599_896 082599 082599_916 082599 082599_917
if you want to calculate the divergence from a specified sequence, your should defined the sequence as MRCA in your group file. You must type "MRCA" (not case-sensitive) in group field (first column) and the name of the sequence in sequence name field (second column):
MRCA name_of_sequence
DIVER generates bootstrapped pseudo data sets from the original data set using PhyML, then returns the bootstrap tree with branch lengths and bootstrap values, using standard NEWICK format. Note that the bootstrap analysis is time consuming process. The maximum number of bootstrapping replicates is set to 100 because of computational resource limitations.
With the bootstrap option off, users can perform approximate likelihood ratio test [1]. This approach is considerably faster than the bootstrap one.
A nucleotide or amino-acid substitution model. DIVER implements a wide range of substitution models via PhyML: GTR (default) [2,3], JC69 [4], K80 [5], F81 [6], HKY85 [7] and TN93 [8] for nucleotide sequences; LG (default) [9], HIVbetween [10], HIVwithin [10], WAG [11], Dayhoff [12], JTT [13], Blosum62 [14], mtREV [15], rtREV [16], cpREV [17], DCMut [18], VT [19], MtArt [20] and MtMAM [21] for amino-acid sequences.
Nucleotide or amino-acid frequencies. They can be optimized (default) or empirical.
Optimized:
Can be fixed with a positive value (default 4.0) or estimated in the maximum likelihood framework. The later makes the program slower. This option is DNA sequences only under HKY85, K80 and TN93 substitution models. The definition of the transition/transversion ratio is the same as in PAML [22]. In PHYLIP, the "transition/transversion rate ratio" is used instead. 4.0 in PHYML roughly corresponds to 2.0 in PHYLIP.
The proportion of invariable sites, i.e., the expected frequency of sites that do not evolve, can be fixed to any value in the 0.0-1.0 range or estimated (default) from the data in the maximum-likelihood framework. The latter makes the program slower.
The different categories correspond to different rates of evolution from site to site. A discrete-gamma distribution is used to account for variation in substitution rates among sites, where the number of categories that defines this distribution can be supplied by the user. The larger this number, the better is the goodness-of-fit as compared to the continuous distribution. The number of categories of this distribution is set to 4 by default, in this case the likelihood of the phylogeny at one site is averaged over four conditional likelihoods corresponding to four rates and the computation of the likelihood is four times slower than with a single rate. Values for number of categories fewer than four or greater than eight are not recommended. In the first case, the discrete distribution is a poor approximation of the continuous one. In the second case, the computational burden becomes high and an higher number of categories is not likely to enhance the accuracy of phylogeny estimation.
The shape of the gamma distribution determines the range of rate variation across sites. This option is used when having more than 1 substitution rate category. Small values, typically in 0.1-1.0 range, correspond to large variability. The higher its value, the lower the variation of substitution rates among sites. The gamma shape parameter can be fixed by the user or estimated (default) via maximum likelihood.
There are three different types to estimate tree topologies. The default approach is to use simultaneous NNI [23]. The second approach relies on subtree pruning and regrafting (SPR) [24]. It generally finds better tree topologies compared to NNI but is also significantly slower. The third approach, Best of NNI & SPR, simply estimates the phylogeny using both methods and returns the best solution among the two.
Optimize tree topology, branch lengths and substitution rate parameters
By default all of three options are optimised in order to maximise the likelihood. There are different combinations that user can choose to optimise.
Users have to provide valid email address to receive the result. Within eamil there is a link to the analysis results.
Calculate diversity and/or divergence based on tree or pairwise distances
Users are allowed to specify whether divergence and diversity are calculated as tree-based (patristic) distances or genetic distances (not conditioned on a tree topology) or both.
Users can provide their own distance matrix to calculate divergence and diversity via DIVER. DIVER accepts two types of distance arrays (matrix and column). The data must be tab delimited.
Examples of matrix:
lower-triangular:
taxa1 taxa2 taxa3 taxa4
taxa1
taxa2 0.0056
taxa3 0.0027 0.0138
taxa4 0.0078 0.0023 0.0123
upper-triangular:
taxa1 taxa2 taxa3 taxa4
taxa1 0.0056 0.0027 0.0078
taxa2 0.0138 0.0023
taxa3 0.0123
taxa4
square:
taxa1 taxa2 taxa3 taxa4
taxa1 0.0000 0.0056 0.0027 0.0078
taxa2 0.0056 0.0000 0.0138 0.0023
taxa3 0.0027 0.0138 0.0000 0.0123
taxa4 0.0078 0.0023 0.0123 0.0000
Example of column:
taxa1 taxa2 0.0056 taxa1 taxa3 0.0027 taxa1 taxa4 0.0078 taxa2 taxa3 0.0138 taxa2 taxa4 0.0023 taxa3 taxa4 0.0123
(A) DIVER output interface from which user can view and download results. (B) Estimated maximum likelihood phylogenetice tree viewed through the ATV Java aplet. (C) Estimated evolutionary parameters. (D) Reconstructed MRCA sequence. (E) Summarized divergence. (F) Plot of divergence. (G) Summarized diversity. (H) Plot of diversity. (I) Distance matrix. (J) Distance distribution histogram. (K) Summarized distances between different groups.
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