PROTML is a main program in MOLPHY for inferring evolutionary trees from PROTein (amino acid) sequences by using the Maximum Likelihood method.
MOLPHY includes several programs, namely:
PROTML: Maximum Likelihood Inference of Protein Phylogeny
NUCML: Maximum Likelihood Inference of Nucleic Acid Phylogeny
PROTST: Basic Statistics of Protein Sequences
NUCST: Basic Statistics of Nucleic Acid Sequences
NJDIST: Neighbor Joining Phylogeny from Distance Matrix

PROTML inference is one of the most popular methods for inferring phylogenetic trees.
It is based on a probabilistic model which assigns a likelihood to a given tree topology.
It is called “Maximum Likelihood” since the maximizing of the likelihood function happens when the observed distribution of the data is the most likely one.
PROTML implements several models (see PROTML Models).
MOLPHY’s PROTEINML Model (PROTML-P) is based on the PROTEINART model (PROTML-PAM), which is an extension of the PROTEIN model.
It was specifically designed to fit the PROTML inference when dealing with sequences with variable substitution rates.
PROTML-P is available in MOLPHY only for rooted trees, but can deal with non-rooted trees as well, thanks to the following editable lines in model.PROTML. (See PROTML Models)
#PROTML-P is the model used for non-rooted trees as well.
#PROTML-P is rooted under the following conditions:
#- the number of sequences in the alignment is even (2, 4, 6, 8,…)
#- an outgroup is present (basically, it is used as a root)
MOLPHY also allows PROTML-P models to be used with non-rooted trees.

The models PROTEINART, PROTOML, PROTOML-2, PROTOML-4, PROTOML-6, PROTML, PROTML-P, and PROTML-PAM are described in their respective Wikipedia articles.

PROTML-P uses the PROTML-PAM model to fit sequence alignment.
Its formula for the likelihood is:

#PDFRootedModel-PAMlikelihood(X,t,n) = NX(X) + NX(x,0) + NDX(N) + N(x,N-1)
+ NNA(X,t) + NNA(NA,t) + NNA(A,t)

PROTML is a main program in Molphy Product Key for inferring evolutionary trees from PROTein (amino acid) sequences by using the Maximum Likelihood method.
PROTML is the unique program in the suite of programs that does not use an E-value to estimate the statistical significance of the topology, or distance, under maximum-likelihood. PROTML assumes that a multiple alignment (a collection of the same or similar amino acids in the same order) as input is evolved under the Maximum Likelihood model. Then PROTML infers an amino acid or nucleic acid tree and makes a fast bootstrapping to estimate the robustness of the maximum-likelihood phylogeny.
PROTML can handle multiple sequence alignment of any length, e.g. thousands of sequences.
PROTML uses Pseudohyphal growth for genome-scale protein sequence multiple alignment.
PROTML uses an ML method and a fast bootstrapping, the cornerstone of the estimation of tree robustness.
The Genetic Code:
CUN(A/K) for the amino acid cysteine(C)
CUA(I/L/M) for the amino acid cysteine(C)
CUG(G/S) for the amino acid cysteine(C)
AUA(I/L/M/V/M/V) for the amino acid isoleucine(I)
AUC(F/L/V) for the amino acid isoleucine(I)
AUU(F/L) for the amino acid phenylalanine(F)
AUA(F/L/V/M) for the amino acid leucine(L)
AUU(F/L) for the amino acid phenylalanine(F)
AUG(G) for the amino acid methionine(M)
UGG(G) for the amino acid tryptophan(W)
UAA(W) for the amino acid tryptophan(W)
AAU(F/L/V/I) for the amino acid valine(V)
AAC(D/E/G/H/I) for the amino acid aspartic acid(D)
ACC(T/S) for the amino acid aspartic acid(D)
ACG(G) for the amino acid glutamic acid(E)
ACU(S
b7e8fdf5c8

MOLPHY is a fast and highly accurate maximum likelihood and Neighbor
Joining software based on the MUSCLE algorithm. It is a distributed
software that can handle the largest number of data files at once. It
implements the Maximum Likelihood, the Neighbor Joining and the Maximum
Likelihood/Neighbor Joining computations. It uses standard statistical
tests to determine the significance of branches in trees.
MOLPHY is a free, open-source and highly efficient program. It
incorporates the MUSCLE algorithm for amino acid alignments which has
been proved to be the fastest software for sequence comparison. MOLPHY
incorporates 2 programs for nucleic acid alignments: MOLPHY-NUCLEOT,
which implements a special maximum likelihood algorithm for nucleotide
alignments, and MOLPHY-NUCLEOT which implements the Neighbor Joining
algorithm for nucleotide alignments.
MOLPHY has been used to study several microorganisms at
laboratories around the world. It has been applied to many gene
sequencing projects. It has also been used to reconstruct phylogenetic
trees using other methods, such as the Maximum Likelihood, Bayesian
Inference and Maximum Parsimony, and has been compared with well-known
software, including PAUP, PHYLIP, PHYML, POY and SplitTree. MOLPHY has
been applied for the reconstruction of phylogenies of many organisms:
chromosomes, prokaryotes, eukaryotes and unicellular species, and even
the reconstruction of trees for which you do not have a high quality
reference tree.
In 1997, a benchmark was used to compare the performance of the
software programs PHYML, PROTML, PAUP, NUCL-ALIGN-2, PHYLIP, DNAPLOT,
PHY-KML, ML-PROBA, SPLIT and SplitTree in reconstructing the phylogeny of
6 organisms. The topology of the reference tree was taken from the
unpublished data from Prof. N.D. Landry (Department of Biology,
McMaster University, Canada). A Mega-algorithm comparison among 9
software programs was performed by applying three tests:
1. Absolute values of splits,
2. Relative values of splits and
3. Degrees of support
The program MOLPHY was found to

PROTML detects L-shaped protein evolutionary trees from the most likely MLE tree topology inferred from the alignment of protein or nucleic acid sequences using the Maximum Likelihood method.
PROTML is developed using Python and R language to speed up the computation.
PROTML includes several functions:
findMaximumLikelihoodTree() to infer MLE tree topology from protein sequence alignment.
findProteinOrNucleicAcidMLEtree() to find most likely protein or nucleic acid MLE tree topology from the input tree topology with distance information.
calculateLRT() to calculate ML-LRT statistic from protein or nucleic acid sequences.
calculateUWLRT() to calculate the unweighted version of ML-LRT statistic.
calculateLRT() to calculate LRT statistic from distance matrix.
findProteinOrNucleicAcidMLETree() is developed using Python and R language to speed up the computation.
PROTML is based on the latest Maximum Likelihood software which can be found on GenomeNet server or as a precompiled package. PROTML now works on the BLOSUM62 matrix and employs an implicit weight parameter in calculating maximum likelihood.
included programs:
NUCML: Maximum Likelihood Inference of Nucleic Acid Phylogeny
PROTST: Basic Statistics of Protein Sequences
NUCST: Basic Statistics of Nucleic Acid Sequences
NJDIST: Neighbor Joining Phylogeny from Distance Matrix
Example
# Infer the most likely protein L-shaped tree using the MLE method
# based on the alignment of three sequences
# the sequences are found on the ‘Uromytins’ branch of
# the ‘Phytolaccaceae’, and aligned using the BLOSUM62 matrix
import numpy as np
from molphy.protml import findMaximumLikelihoodTree, findProteinOrNucleicAcidMLETree

def main():
# Calculate the maximum likelihood for L-shaped protein tree from
# the 3 sequences
L=findMaximumLikelihoodTree(np.genfromtxt(‘S1_s0.dna’, header=None),

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