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1

Rename node

RenameSeq - Rename sequence names in FASTA file and
save original names into separate file


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Input
Codon sequences in FASTA format (example shown
for direct rename). For reverse rename any text
files can be used (trees, alignment with
reconstructed ancestors, etc.).
Load a local file with data

Alternatively, paste here
Example
Input
Legenda file 		Load a local file with data

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Input
Divergence dates file
Load a local file with data

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Example
Rename
Direct or reverse rename

2

Alignment node

Mafft - Accurate multiple sequence alignment algorithm
based on fast Fourier transform (Katoh and Toh, 2008)
with BLOSUM (Henikoff, Henikoff, 1992) or PAM (Dayhoff et al., 1978) or
transmembrane PAM (Jones et al., 1994) matrices


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Input
Protein sequences in FASTA format
Load a local file with data

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Example
Alignment strategy
Fastest - progressive method with a rough guide
tree; Local - iterative refinement method
incorporating local pairwise alignment
information; Global - iterative refinement
method incorporating global pairwise alignment
information; Biggaps - iterative refinement
method incorporating local pairwise alignment
information with the generalized affine gap cost
Select matrix
Matrices for alignment
BLOSUM matrix
BLOSUM matrix (Henikoff and Henikoff, 1992)
PAM matrix
PAM matrix number (Dayhoff et al., 1992):
number>0
Transmembrane PAM matrix
Transmembrane PAM number (Jones et al., 1994)
matrix: number>0.

Kalign - Multiple sequence alignment algorithm designed to
fast alignment of large numbers of protein sequences
(Lassmann and Sonnhammer, 2005)
Method references:
Wu-Manber approximate string-matching algorithm (Wu and Manber, 1992),
Dynamic programming (Eddy, 2004)


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Input
Protein sequences in FASTA format
Load a local file with data

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Example
Gap open penalty
Gap open penalty
Gap extension penalty
Gap extension penalty
Terminal gap penalties
Terminal gap penalties
A constant added to the substitution matrix
A constant added to the substitution matrix
Methods
Wu and Manber or Dynamic programming

3

Amino acid substitution model estimation

Modelestimator - Amino acid substitution model estimation
from alignment (Arvestad, 2006)


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Input
Protein sequence alignment in FASTA format
Load a local file with data

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Example
Use gaps in analysis
Use gaps in model estimation
Calculation precision
Calculation precision

4

Build tree node

FastTree - Approximately Maximum-Likelihood Trees for Large Alignments
(Price et al., 2010)
CAT model (Lartillot and Philippe, 2004).
Tree selection criteria:
Minimum-Evolution (Rzhetsky and Nei, 1992),
Maximum-Likelihood (Aldrich, 1997).
Branch supports:
Shimodaira-Hasegawa test (Shimodaira and Hasegawa, 1999),
Bootstrap (Felsenstein, 1985).
Tree search algorithm:
Subtree pruning and regrafting (SPR) (Hordijk and Gascuel, 2005).


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Input
Protein sequence alignment in FASTA format
Load a local file with data

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Example
Input
Starting tree in Newick format (without branch
support values)
Load a local file with data

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Example
Analysis type
From starting tree or de novo
Branch support
Shimodaira-Hasegawa-like branch support
(Maximum-Likelihood) or minimum-evolution
bootstrap supports
Reconstruction method
Maximum-Likelihood; Minimum-Evolution;
Maximum-Likelihood optimization of branch lengths
for a Fixed Topology
Number of rate categories
Specify the number of rate categories (CAT) of
sites
Branch lengths deep optimization
after optimizing the tree under the CAT
approximation, rescale the lengths to optimize
the Gamma20 likelihood

Phyml - A simple, fast, and accurate algorithm to estimate
large phylogenies by maximum likelihood approach (Guindon and Gascuel, 2003;
Quang et al, 2008)
Amino acid substitution models:
LG (Le and Gascuel, 2008),
WAG (Whelan and Goldman, 2001),
JTT (Jones at al., 2001),
Blosum62 (Henikoff and Henikoff, 1992),
Dayhoff (Dayhoff et al., 1978),
DCMut (Kosiol and Goldman, 2005),
VT (Muller and Vingron, 2000),
CpREV (Adachi et al., 2000),
MtREV (Adachi and Hasegawa, 1996),
RtREV (Dimmic et al., 2002),
MtMam (Cao et al., 1998),
MtArt (Abascal et al., 2007),
HIVw and HIVb (Dang et al., 2009),
Mixture Models (Le et al, 2008)
CAT model (Lartillot and Philippe, 2004).
Branch supports:
Approximate likelihood ratio (aLRT) and aLRT with Chi2 (Anisimova and Gascuel, 2006),
Shimodaira-Hasegawa (Shimodaira and Hasegawa, 1999).
Tree selection criteria:
Maximum-Likelihood (Aldrich, 1997).
Tree search algorithm:
Subtree pruning and regrafting (SPR) (Hordijk and Gascuel, 2005),
Nearest neighbor interchange (NNI).


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Input
Protein sequence alignment in FASTA format
Load a local file with data

Alternatively, paste here
Example
Input
Starting tree in Newick format (without branch
support values)
Load a local file with data

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Example
Input
Amino acid substitution model (PAML format)
Load a local file with data

Alternatively, paste here
Example
Analysis type
De novo; From starting tree; From specific amino
acid substitution model; From starting tree and
specific amino acid substitution model
Sequence format
Interleaved (default) or Sequential
Branch support
Approximate likelihood ratio test returning aLRT
statistics; Approximate likelihood ratio test
returning Chi2-based parametric;
Shimodaira-Hasegawa-like branch support; No
statistical support
Model
General Amino acid substitution model, CAT models
= C10-C60, Mixture Models = EX2, EX3, EHO, UL2
and UL3.
Proportion of invariable sites
Proportion of invariable sites, a fixed value
(between 0.0 and 1.0) or 'e' to get the maximum
likelihood estimate
Value of the gamma shape parameter
Can be a fixed positive value or 'e' to get the
maximum likelihood estimate
Number of relative substitution rate categories
Must be small integer
Tree topology search operation option
Can be either NNI (default, fast) or SPR (a bit
slower than NNI) or BEST (best of NNI and SPR
search)
Optimization schema
Can be a combination of tree topology (t), branch
length (l) and substitution rate parameters (r)
are optimised

5

Gaps delete node

GapsDel - Deleting gaps from alignment


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Input
Protein sequence alignment in FASTA format
Load a local file with data

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Example

6

Ancestral reconstruction node

Ancescon - Ancescon (Cai et al., 2004) ancestor reconstruction
under WAG substitution model (Whelan and Goldman, 2001),
Marginal reconstruction method (Koshi and Goldstein, 1996)


Show/Hide input files
Input
Protein gapless sequence alignment in FASTA
format
Load a local file with data

Alternatively, paste here
Example
Input
Unrooted tree in Newick format
Load a local file with data

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Example
Alfa optimization
Optimize alfa by maximum likelihood (O) or
calculate correlated alfa (C)
Dan method
Use Dan method to find the optimal solution

Fastml - Fastml (Pupko et al., 2002) ancestor reconstruction
under various general substitution models,
Marginal reconstruction method (Koshi and Goldstein, 1996)
Amino acid substitution models:
LG (Le and Gascuel, 2008),
WAG (Whelan and Goldman, 2001),
JTT (Jones at al., 2001),
Dayhoff (Dayhoff et al., 1978),
CpREV (Adachi et al., 2000),
MtREV (Adachi and Hasegawa, 1996),
Jukes-Cantor (Jukes and Cantor, 1969).


Show/Hide input files
Input
Protein gapless sequence alignment in FASTA
format
Load a local file with data

Alternatively, paste here
Example
Input
Unrooted tree in Newick format
Load a local file with data

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Example
Number of gamma rate categories
Specify the number of gamma rate categories
Alpha fixation
Alpha is fixed
Alpha parameter
Alpha parameter of the gamma distribution
(initial or fixed)
Optimize branch
Optimize branch lengths on starting tree
Model
General Amino acid substitution model

Codeml - Codeml (Yang, 2007) ancestor reconstruction under
various general and user defined substitution model,
Marginal reconstruction method (Koshi and Goldstein, 1996)
Amino acid substitution models:
LG (Le and Gascuel, 2008),
WAG (Whelan and Goldman, 2001),
JTT (Jones at al., 2001),
Dayhoff (Dayhoff et al., 1978),
DCMut (Kosiol and Goldman, 2005),
CpREV (Adachi et al., 2000),
MtREV (Adachi and Hasegawa, 1996),
MtMam (Cao et al., 1998),
MtArt (Abascal et al., 2007),
MtZoa (Rota-Stabelli al., 2009).


Show/Hide input files
Input
Protein gapless sequence alignment in FASTA
format
Load a local file with data

Alternatively, paste here
Example
Input
Unrooted tree in Newick format
Load a local file with data

Alternatively, paste here
Example
Input
Amino acid substitution model (PAML format)
Load a local file with data

Alternatively, paste here
Example
Analysis type
On the basis of general model or on the basis of
user defined model
Number of gamma rate categories
Specify the number of gamma rate categories
Alpha fixation
Alpha is fixed
Alpha parameter
Alpha parameter of the gamma distribution
(initial or fixed)
Model type
Model type
Models
General Amino acid substitution models

7

Rare changes detection node

RareMap - Detection of rare amino acid changes using comparison of
protein evolution model (INDELible: Fletcher and Yang, 2009)
with real data through nonparametric permutation test
(Gunbin et al., 2009)
Amino acid substitution models:
LG (Le and Gascuel, 2008),
WAG (Whelan and Goldman, 2001),
JTT (Jones at al., 2001),
Blosum (Henikoff and Henikoff, 1992),
Dayhoff (Dayhoff et al., 1978),
DCMut (Kosiol and Goldman, 2005),
VT (Muller and Vingron, 2000),
CpREV (Adachi et al., 2000),
MtREV (Adachi and Hasegawa, 1996),
RtREV (Dimmic et al., 2002),
MtMam (Cao et al., 1998),
MtArt (Abascal et al., 2007),
HIVw and HIVb (Dang et al., 2009).


Show/Hide input files
Input
Unrooted tree in Newick format with branch
lenghts
Load a local file with data

Alternatively, paste here
Example
Input
Tree in Newick format with ancestors labels
Load a local file with data

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Example
Input
FASTA protein sequence alignment with
reconstructed ancestors
Load a local file with data

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Example
Input
Probabilities of reconstructed sites
Load a local file with data

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Example
Input
Amino acid substitution model (PAML format)
Load a local file with data

Alternatively, paste here
Example
Input
Advanced clade model of evolution (INDELible
format)
Load a local file with data

Alternatively, paste here
Example
Analysis type
On the basis of general model (simple or
advanced); On the basis of user defined model
(simple or advanced)
Models
General Amino acid substitution models or equal
substitution rates (Poisson)
Number of gamma rate categories
Specify the number of gamma rate categories
Alpha parameter
Alpha parameter of the gamma distribution
(initial or fixed)
Probability
Probability threshold
Permutation
Permutations number
Replicates
Number of replicates
Modeled alignment lenght
Modeled alignments lenght
Invariable sites for modelling
Proportion of invariable sites for modelling

8

Evolutionary changes analysis node

ChangesSum - Summing up evolutionary changes

Evolutionary distance corrections:
Gamma (Ota and Nei, 1994),
Kimura (Kimura, 1983),
Jukes-Cantor (Jukes and Cantor, 1969).


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Input
Tree with rare changes
Load a local file with data

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Example
Input
Tree in Newick format with ancestors labels
Load a local file with data

Alternatively, paste here
Example
Input
FASTA protein sequence alignment with
reconstructed ancestors
Load a local file with data

Alternatively, paste here
Example
Input
Legenda file
Load a local file with data

Alternatively, paste here
Example
Analysis type
Test for all amino acid property changes (all) or
Test for rare amino acid property changes (rare)
Alpha parameter
Alpha parameter of the gamma distribution for
gamma distance correction or Kimura correction
(KC) or Jukes-Cantor correction (JCC)

9

Fast chronogram building node

r8s - (Sanderson, 2003). Constructing relaxed molecular clock
tree using Nonparametric rate smoothing - NPRS (Sanderson, 1997)
or Penalized likelihood, PL, approaches (Sanderson, 2002)
You must enter rooted tree for chronogram construction!


Show/Hide input files
Input
Codon sequence alignment in FASTA format
Load a local file with data

Alternatively, paste here
Example
Input
Manually rooted tree in in Newick format (without
branch support values)
Load a local file with data

Alternatively, paste here
Example
Input
Divergence dates file
Load a local file with data

Alternatively, paste here
Example
Input
Gamma parameter (alpha) 		Load a local file with data

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Input
Advanced r8s model (Nexus formatted file, see r8s
manual)
Load a local file with data

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Example
Analysis type
simple or advanced
Analysis method
NPRS or PL
Penalty function
logarithmic or additive
num_time_guesses
Number of initial starts, using different random
combinations of divergence times (less than 50)
num_restarts
Number of perturbed restarts after initial
solution is found (less than 50)
perturb_factor
Fractional perturbation of parameters during
restart (less than 0.1)
minRateFactor
Imposed lower bound on the rates as a fraction of
the approximate mean rate (less than 0.1)
minDurFactor
Imposed lower imposed lower bound on the
durations of 0-length terminal branches as a
fraction of root age (less than 0.01)
activeEpsilon
Tolerance level set for the gradient solution -
activeEpsilon (less than 0.01)

10

Phylogenetic comparative statistics node

Stattests - Phylogenetic statistic tests for evolutionary correlation
between molecular and phenotypical characteristics R: ape
You must enter quantitative phenotypical data for statistical analysis!
Methods for comparative analyses of data in a phylogenetic framework:
GEE (Paradis and Claude, 2002),
Lynch (Lynch, 1991),
Blomberg (Blomberg at al., 2003),
Martins (Martins and Hansen, 1997),
Grafen (Grafen, 1989),
Pagel (Pagel, 1999),
Brownian (Felsenstein, 1985).


Show/Hide input files
Input
Amino acid property changes (tab delimited)
Load a local file with data

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Example
Input
Molecular clock-like tree in Newick format
Load a local file with data

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Example
Input
Legend file
Load a local file with data

Alternatively, paste here
Example
Analysis type
GLS (selection between Brownian, Pagel, Blomberg,
Grafen, Martins methods on the basis of BIC
[test1 file] and AICc [test2 file]), Lynch or GEE
Phenotypical data
User defined phenotypical data (space delimited;
in the same order as leaves on the phylogenetic
tree; as many values as leaves on the
phylogenetic tree)


Pipeline
scheme