Start:    Stop:


1

Rename node

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


Show/Hide input files
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

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

Alternatively, paste here
Example
Rename
Direct or reverse rename

2

Codons to Amino acids Translation node

Transeq - Translate nucleic acid sequences into proteins
(Rice et al., 2000)


Show/Hide input files
Input
DNA multifasta
Load a local file with data

Alternatively, paste here
Example
Genetic code
Values: 0 (Standard); 1 (Standard (with
alternative initiation codons)); 2 (Vertebrate
Mitochondrial); 3 (Yeast Mitochondrial); 4 (Mold,
Protozoan, Coelenterate Mitochondrial and
Mycoplasma/Spiroplasma); 5 (Invertebrate
Mitochondrial); 6 (Ciliate Macronuclear and
Dasycladacean); 9 (Echinoderm Mitochondrial); 10
(Euplotid Nuclear); 11 (Bacterial); 12
(Alternative Yeast Nuclear); 13 (Ascidian
Mitochondrial); 14 (Flatworm Mitochondrial); 15
(Blepharisma Macronuclear); 16 (Chlorophycean
Mitochondrial); 21 (Trematode Mitochondrial); 22
(Scenedesmus obliquus); 23 (Thraustochytrium
Mitochondrial)

3

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


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

Alternatively, paste here
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)


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

Alternatively, paste here
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
Distance method
Distance method

4

Amino acid substitution model estimation

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


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

Alternatively, paste here
Example
Use gaps in analysis
Use gaps in model estimation
Calculation precision
Calculation precision

5

Amino acids to Codons Translation node

Tranalign - Translate nucleic acid sequences into proteins
(Rice et al., 2000)


Show/Hide input files
Input
Protein FASTA alignment 		Load a local file with data

Alternatively, paste here
Input
DNA multiple sequences in FASTA format 		Load a local file with data

Alternatively, paste here
Genetic code
Values: 0 (Standard); 1 (Standard (with
alternative initiation codons)); 2 (Vertebrate
Mitochondrial); 3 (Yeast Mitochondrial); 4 (Mold,
Protozoan, Coelenterate Mitochondrial and
Mycoplasma/Spiroplasma); 5 (Invertebrate
Mitochondrial); 6 (Ciliate Macronuclear and
Dasycladacean); 9 (Echinoderm Mitochondrial); 10
(Euplotid Nuclear); 11 (Bacterial); 12
(Alternative Yeast Nuclear); 13 (Ascidian
Mitochondrial); 14 (Flatworm Mitochondrial); 15
(Blepharisma Macronuclear); 16 (Chlorophycean
Mitochondrial); 21 (Trematode Mitochondrial); 22
(Scenedesmus obliquus); 23 (Thraustochytrium
Mitochondrial)

6

Build tree node

FastTree_n -
Approximately Maximum-Likelihood Trees for Large Alignments
(Price et al., 2010)
GTR model (Rodriguez et al., 1990).
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).


Show/Hide input files
Input
Nucleotide FASTA alignment
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

Alternatively, paste here
Example
Analysis type
From starting tree or de novo
Branch support
Shimodaira-Hasegawa 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_n -
A simple, fast, and accurate algorithm to estimate
large phylogenies by maximum likelihood approach (Guindon and Gascuel, 2003;
Quang et al, 2008)
Nucleotide substitution models:
GTR (Rodriguez et al., 1990),
HKY85 (Hasegawa et al., 1985),
K80 (Kimura, 1980),
JC69 (Jukes and Cantor, 1969),
F81 (Felsenstein, 1981),
F84 (Kishino and Hasegawa, 1989),
TN93 (Tamura and Nei, 1993).
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).


Show/Hide input files
Input
Nucleotide FASTA alignment
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

Alternatively, paste here
Example
Analysis type
De novo; From starting tree
Sequence format
Interleaved (default) or Sequential
Branch support
Approximate likelihood ratio test returning aLRT
statistics; Approximate likelihood ratio test
returning Chi2-based parametric; SH-like branch
support; No statistical support
Model
Nucleotide substitution models
Transition/Transversion ratio
Transition/Transversion ratio, a fixed value
(between 0.0 and 1.0) or 'e' to get the maximum
likelihood estimate
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

7

Gaps delete node

GapsDel - Deleting gaps from alignment


Show/Hide input files
Input
Nucleotide fasta alignment
Load a local file with data

Alternatively, paste here
Example

8

Ancestral reconstruction node

ANC-GENE - Ancestor gene reconstruction under constrains of amino acids
changes (Zhang and Nei 1997; Zhang et al., 1998)
First, Distance based Bayesian method applied for ancestral
proteins reconstruction, than parsimony applied for codons inference.
Universal genetic code only.
Amino acid substitution models:
LG (Le and Gascuel, 2008),
WAG (Whelan and Goldman, 2001),
JTT (Jones at al., 2001),
CpREV (Adachi et al., 2000),
MtREV (Adachi and Hasegawa, 1996),
MtZoa (Rota-Stabelli al., 2009).


Show/Hide input files
Input
Codon sequence gapless 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
Load a local file with data

Alternatively, paste here
Example
Analysis type
General or user defined amino acid substitution
matrix
Ancestral search mode
Analysis of All pathways, number of sequences is
up to 8 (1), Extended parsimony pathways, number
of sequences between 9 and 16 (2) Node by node,
number of sequences is more than 17 (3)
Model
General amino acids substitution model or equal
substitution rates (Poisson)

Fastml_n - Fastml (Pupko et al., 2002) ancestor reconstruction
under two codon evolution models, Marginal reconstruction
method (Koshi and Goldstein, 1996), Universal genetic code only.
Codon evolution models:
M5 (Yang et al., 2000),
Empirical (Schneider et al., 2005).


Show/Hide input files
Input
Codon sequence gapless 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
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
Codon evolution model (M5 or Empirical model)

Codeml_n - Codeml (Yang, 2007) ancestor reconstruction under
various modification of M8 (Yang et al., 2000) codon evolution model,
Marginal reconstruction method (Koshi and Goldstein, 1996)


Show/Hide input files
Input
Codon sequence gapless 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
Genetic code
0 for the universal code, 1 for the mammalian
mitochondrial code, 3 for mold mt, 4 for
invertebrate mt, 5 for ciliate nuclear code, 6
for echinoderm mt, 7 for euplotid mt, 8 for
alternative yeast nuclear, 9 for ascidian
mt, and 10 for blepharisma nuclear
Number of categories
Number of categories for beta and w codon
substitution model (M8)
Kappa (Ts/Tv) fixation
Kappa is fixed
Kappa (Ts/Tv) parameter
Kappa (Ts/Tv) parameter (initial or fixed)
Omega (Ka/Ks) fixation
Omega is fixed
Omega (Ka/Ks) parameter
Omega (Ka/Ks) (initial or fixed)
Codon frequencies in codon substitution model
Equal (0), Calculated from the average nucleotide
frequencies (1), From the average nucleotide
frequencies at the three codon positions (2),
Used as free parameters (3)

9

Kr/Kc estimation node

HON-NEW - Calculation of Kr, Kc, Kr/Kc, and variances of Kr and Kc
(Zhang, 2000)
using all possible amino acid groupings in compliance with it's all
known physicochemical properties (Kawashima et al., 2008)


Show/Hide input files
Input
FASTA alignment with reconstructed ancestors
Load a local file with data

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

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

Alternatively, paste here
Example
Ts/Tv
Transition transversion ratio: estimated(e) or
user defined
Amino acid partitioning
Number of amino acid classes

SMITH - Calculation of Kr, Kc, Kr/Kc
(Smith, 2003)
using all possible amino acid groupings in compliance with it's all
known physicochemical properties (Kawashima et al., 2008)
or using BLOSUM substitution matrix (Henikoff, Henikoff, 1992)


Show/Hide input files
Input
FASTA alignment with reconstructed ancestors
Load a local file with data

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

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

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

Alternatively, paste here
Example
Analyzing mode
BLOSUM matrix or ALL amino acid partitioning
Amino acid partitioning
Number of amino acid classes

10

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

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

Alternatively, paste here
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)

11

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
Kr/Kc or Kr or Kc values (tab delimited)
Load a local file with data

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

Alternatively, paste here
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)

12

Neutral Kr/Kc estimation node

HON-NEUTRAL - Calculation of mean and standart
deviations of Kr, Kc, Kr/Kc (Zhang, 2000) under neutral
evolution conditions (Ka/Ks=1) simulated by INDELible (Fletcher and Yang, 2009),
using all possible amino acid groupings in compliance with it's all
known physicochemical properties (Kawashima et al., 2008)


Show/Hide input files
Input
FASTA gapless DNA alignment
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
Tree in Newick format with ancestors labels
Load a local file with data

Alternatively, paste here
Example
Input
Legend file
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 automatically generated model
using PAML CODEML parameter estimation (auto); On
the basis of user defined model (user)
Ts/Tv
Transition transversion ratio (for simulation and
simulated data analizing): estimated by HON-NEW
node (HON), estimated by PAML CODEML (PAML), or
user defined
Iterations number
Iterations number
Amino acid partitioning
Number of amino acid classes
Genetic code
0 for the universal code, 1 for the mammalian
mitochondrial code, 3 for mold mt, 4 for
invertebrate mt, 5 for ciliate nuclear code, 6
for echinoderm mt, 7 for euplotid mt, 8 for
alternative yeast nuclear, 9 for ascidian mt,
and 10 for blepharisma nuclear

SMITH-NEUTRAL - Calculation of mean and standart
deviations of Kr, Kc, Kr/Kc (Smith, 2003) under neutral
evolution conditions (Ka/Ks=1) simulated by INDELible (Fletcher and Yang, 2009),
using all possible amino acid groupings in compliance with it's all
known physicochemical properties (Kawashima et al., 2008)
or using BLOSUM substitution matrix (Henikoff, Henikoff, 1992)


Show/Hide input files
Input
FASTA gapless DNA alignment
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
Tree in Newick format with ancestors labels
Load a local file with data

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

Alternatively, paste here
Example
Input
Blosum MATRIX
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 automatically generated model
using PAML CODEML parameter estimation (auto); On
the basis of user defined model (user)
Ts/Tv
Transition transversion ratio (for simulation
only): estimated by PAML CODEML (PAML), or user
defined
Iterations number
Iterations number
Analyzing mode
BLOSUM matrix or ALL amino acid partitioning
Amino acid partitioning
Number of amino acid classes
Genetic code
0 for the universal code, 1 for the mammalian
mitochondrial code, 3 for mold mt, 4 for
invertebrate mt, 5 for ciliate nuclear code, 6
for echinoderm mt, 7 for euplotid mt, 8 for
alternative yeast nuclear, 9 for ascidian mt,
and 10 for blepharisma nuclear


Pipeline
scheme