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
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MOLPHY is a package which makes available for the scientific community, through a
unified interface, the methods for inferring phylogenetic trees from unaligned data
either in the DNA (Nucleic Acids) or in the protein (Proteins) frame. MOLPHY is
based on MOLPHY , a Fast, Accurate and Portable Phylogeny Package for
UNIX-like Workstations running the Linux operating system (Linux is the most
widely distributed free UNIX-like operating system). The web site of the package
can be found at:
The purpose of MOLPHY is to provide a ready-to-use application, working either
as a stand-alone application or as part of a pipeline for reconstructing and
comparison of phylogenies, given a set of possibly poorly aligned sequences.
PROTML (Maximum Likelihood Inference of Protein Phylogeny) is a part of
MOLPHY package, which belongs to the following sections:
INTRODUCTION TO PROTML
PROTML is a software package for inferring protein phylogenies by using the
Maximum Likelihood method. PROTML is based on the Maximum Likelihood method
(ML), of inferring the phylogeny using unaligned sequence data. For the last
decades, the Maximum Likelihood method has been the standard for inferring
protein phylogenies, and it is the one which is usually used by existing
pipelines. MOLPHY also offers the Neighbor Joining (NJ) method for the
inferring of DNA (nucleic acid) phylogenies. MOLPHY is distributed as a
stand-alone application. MOLPHY is a fast, accurate and portable
phylogeny package which can be used on UNIX-like workstations. MOLPHY is
written in C.
The program includes several software, namely: PROTML:
Phylogenetic tree inference program which can be run either directly (as a
stand-alone application) or as part of a pipeline.
PROTST: Basic Statistics of Protein Sequences, including:
The command to compute a protein (amino acid) sequence database (
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PROTML is based on the method described by Maddison and Maddison (1996, Study of phylogenetic trees from proteins. in Phylogenetic analysis: The state of the art. B.H. Maddison and R.T. Maddison, eds. Taylor and Francis, London, 473–490.
MOLPHY is publicly available for Unix and Windows platforms. See
Submit a protein sequence on a single page. MOLPHY reads the sequences on a separate web page, designed for testing the program, and saves them on a local disk. Enter the URL of your submission on this page:
Don’t forget to fill out the authentication form which asks for your e-mail and name.
These tables give details for the kinds of sequence submission that MOLPHY allows.
This form allows you to create web pages where users can submit their queries.
Submission page URL:
In this example you will have to fill out the submission URL first, and then add the rest of the information for the submission page URL.
Note: This URL must be an existing web page.
This is the URL where the user will be submitting his query or his input file.
This is the input file or the URL to the input file of the query.
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PROTML and MOLPHY are based on the so-called Maximum Likelihood method.
The Maximum Likelihood (ML) method allows to determine an evolutionary tree (cladogram) under a so-called Maximum Parsimony criterion.
As an alternative to the Maximum Likelihood method, the so-called Neighbor Joining (NJ) method (constructed by Saitou and Nei in 1987) and the Minimum Evolution (ME) method have been proposed. These are computationally less demanding methods, but they are not considered to be statistically better methods than the ML method (see for example Felten et al., 1995).
MOLPHY deals with the Maximum Likelihood method in particular. Several papers are based on the Maximum Likelihood method (see for example: Brian Thomas and Michael F. Smith, Subtree-Pruning-Regrafting, a Two-Called Algorithm, in Proceedings of the 6th Annual Carnegie-Mellon Conference on Phylogenetics, 1987; M. C. Silva and K. Strimmer, A heuristic search strategy for multi-sequence alignment using the maximum likelihood approach, in Proceedings of the Third Annual Workshop of the Canadian Society for Bioinformatics and Computational Biology, page 5; and Guido V. Cavalli-Sforza and Kent A. R. Godfrey, Phylogenetic analysis using the maximum likelihood method, p. 759 in Current Topics in Microbiology and Immunology, Ed. M. S. Rubin, A Wiley-Interscience publication, 1992).
PROTML is an application of MOLPHY (created by F. Le Gros et al.).
It is possible to infer the phylogenetic tree of protein sequences (amino acids) under the Maximum Likelihood (ML) method by using PROTML.
When it is possible to infer the phylogenetic tree of protein sequences (amino acids) under the Maximum Likelihood (ML) method, PROTML will automatically use this method.
PROTML computes all models of amino acid replacement given a phylogenetic tree. It has been found by previous publications that the best model is the one that maximizes the likelihood of all amino acid data given a phylogenetic tree.
FIG. 1 shows the different steps performed by PROTML, consisting of a preparation phase and a main loop.
During the preparation phase, a user (e.g. a researcher, an expert) can prepare a phylogenetic tree (or
What’s New in the Molphy?
Transfer to Jupyter Notebooks for Data Science
I am currently trying to explore data visualization on Python using Jupyter Notebook. I have a dataset and I’d like to process it via several data prep-steps such as read in & preprocessing.
I am wondering whether, within the Jupyter Notebook, I can have my data preprocessing code also be used for future data visualization via plotly. Is there a way to export the Jupyter Notebook and use it as a Python script file with name.py (i.e. Python script) to make it portable?
Thanks in advance!
You can use nbconvert to convert your Jupyter Notebook to a Python script.
First, convert your notebook to the JSON format. This can be done using the following command,
jupyter nbconvert –to script my_notebook.ipynb
Next, copy the generated Python script and name it as you like (e.g., my_notebook.py).
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