Error When Opening File Codeml Ctl
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faq • rss Community Log In Sign Up Add New Post Question: PAML input file format 0 23 months ago by The Last Word • 90 India The Last Word • 90 wrote: Hi, I have two files with paml codeml about 4 fasta sequences each in the PHYLIP format for Da/Ds (Ka/Ks) comparison. After a
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search on the net, I found that the best software to do so is PAML and it requires a control file and
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2 input files. For the tree input, I used PHYML which accepts PHYLIP file inputs and gives NEWICK format outputs. However I am unsure as to how to get the sequence file. I tried the sequential format but
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it gives me the "Error in sequence data file" error. This is my control file: my sequence file my tree file Could I get some advice on what is wrong with my input file please. Also, this is just one set of the sequences which I wanted to compare. How do I compare two sets of sequences for the Da/Ds values. I know that this might be basic so thank you for your patience. paml dn/ds tutorial paml file format • 3.5k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 8 months ago by jhc • 2.2k • written 23 months ago by The Last Word • 90 3 23 months ago by Siva • 1.4k United States Siva • 1.4k wrote: I don't think your sequence file is in correct format and does not look like a multiple alignment. You need a multiple sequence alignment as input. You can use the online tools (either Readseq or Built-in coverter) at Phylogeny.fr website to check if your sequence file is in correct format (by trying to convert to other format). The sequences in your file are also not of same length. If the 'cleandata' option is set to 1 in the .ctl file (which is the default), PAML will remove any sites with gaps in at least one sequence. From the PAML User Guide (Page 11): The way that ambiguity characters and alignment gaps are treated in baseml and codeml depends on the variable cleandata in the control file. In the maximum likelihood analysis, sites at which at least one sequence involves an ambiguity character are removed from all sequences before analysis if cleandata = 1, while if cleandata = 0, both ambiguity characters and alignment gaps are treated as ambiguity char
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interface to the PAML (Phylogenetic Analysis by Maximum Likelihood) package of http://biopython.org/wiki/PAML programs. Currently, interfaces to the programs codeml, baseml http://web.mit.edu/6.891/www/lab/paml.html and yn00 as well as a Python re-implementation of chi2 have been included. Availability This module is available in Biopython 1.58 and later. To use this module, you must have PAML version 4.1 error when or greater installed on your system. codeml The codeml interface is provided in the following module: from Bio.Phylo.PAML import codeml The Codeml object Initialization The interface is implemented as an object which maintains program options. In order to error when opening run codeml, typically one provides a control file which indicates the locations of an alignment file, a tree file and an output file, along with a series of options dictating how the software is to be run. In the Codeml object, the three file locations are stored as string attributes. The three file locations, as well as the location of the desired working directory, may be specified in the Codeml constructor as follows: cml = codeml.Codeml(alignment = "align.phylip", tree = "species.tree", out_file = "results.out", working_dir = "./scratch") They may also be set individually: cml = codeml.Codeml (pamlDOC.pdf) PAML FAQs (pamlFAQs.pdf) PAML Resources on the web Questions and Bug Reports Introduction PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/MAC OS X, and executables are provided for MS Windows. This document is about downloading and compiling PAML and getting started. See the manual (pamlDOC.pdf) for more information about running programs in the package. Possible uses of the programs are Estimation of branch lengths in a phylogenetic tree and parameters in the evolutionary model such as the transition/transversion rate ratio, the shape parameter of the gamma distribution for variable evolutionary rates among sites, and rate parameters for different genes; Test of hypotheses concerning sequence evolution, such as rate constancy and independence among nucleotide or amino acid sites, rate constancy among lineages (the molecular clock), and homogeneity of evolutionary process in multiple genes; Calculation of substitution rates at sites; Reconstruction of ancestral nucleotide or amino acid sequences; Simulation of nucleotide, codon, and amino acid sequence data sets; Phylogenetic tree reconstruction by maximum likelihood and Bayesian methods (??). A summary of the types of analyses performed by different programs in the package is given below. baseml: ML analysis of nucleotide sequences: estimation of tree topology, branch lengths, and substitution parameters under a variety of nucleotide substitution models (JC69, K80, F81, F84, HKY85, TN93, REV); constant or gamma rates for sites; molecular clock (rate constancy among lineages) or no clock, among-gene and within-gene variation of substitution rates; models for combined analyses of multiple sequence data sets; calculation of substitution rates at sites; reconstruction of ancestral nucleotides. basemlg: ML analysis of nucleotide sequences under the model of gamma rates among sites. The (continuous) gamma model is used with one of the following substitution models: JC69, K80, F81, F84, HKY85, TN93, and REV. codonml (codeml with seqtype = 1): ML analysis of protein-coding DNA sequences using codon substitution models (e.g., Goldman and Yang 1994); calculation of the codon-usage table; estimation of synonymous and nonsynonymous substitution rates; likelihood ratio test of positive selection or relaxed selec