Search Results for "phylogenetic"
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Showing 99 open source projects for "phylogenetic"
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...Its main functionalities include: - Mining single-copy nuclear genes, plastid genes/genomes, and other molecular markers from next-generation sequencing data. - Aligning and trimming multiple molecular markers, constructing concatenated and coalescent-based phylogenetic trees, and calibrating tree time. Reference for GeneMiner2: Yu XY, Tang ZZ, Zhang Z, Song YX, He H, Shi Y, Hou JQ, Yu Y. 2026. GeneMiner2: Accurate and automated recovery of genes from genome-skimming data. Molecular Ecology Resources 26: e70111.https://doi.org/10.1111/1755-0998.70111
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com-hfg
java library for XML, HTML, or SVG generation + bioinformatics classes
The com.hfg (hairyfatguy.com) library is a collection of utility classes that make it easy to construct XML, HTML, XHTML, or SVG in an object-oriented way from within your Java application or webapp. It also contains other IO utilities and bioinformatics classes for phylogenetic trees, taxonomy, and multi-chain proteins. Requires JDK1.8. -
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CPAT
RNA coding potential assessment tool
...However, Most previous coding potential prediction methods heavily rely on alignment, either pairwise alignment to search for protein evidence or multiple alignments to calculate phylogenetic conservation score (such as CPC , PhyloCSF and RNACode ). This is because most previously identified transcripts including protein coding RNA and short, housekeeping/regulatory RNAs such as snRNAs, snoRNA and tRNA are highly conserved. While still very useful, these approaches have several limitations: Most lncRNAs are less conserved and tend to be lineage specific which greatly limit the discrimination power of alignment-based methods. ... -
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP4 can take 100's of microbial genomes as input. A SNP locus is defined by an oligo of length k surrounding a central SNP allele. kSNP4 can analyze both complete (finished) genomes and unfinished genomes in assembled contigs or raw, unassembled reads. ... -
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Nexplorer is a web-based phylogenetic browser, used to view and edit comparative data, and ideal for creating publication-quality views in which the tips of a tree are aligned with the rows of a character matrix (e.g., a sequence alignment).
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TaxOnTree
A program for associating taxonomic information in a phylogenetic tree
TaxOnTree is a phylogenetic program for associating Taxonomic information in a phylogenetic tree. The output is a NEX format tree file configured to be opened in FigTree, that users can promptly color by any taxa or by the ancestrality shared by sequences with query. Input can be a Fasta formatted file to be used in a BLAST search or a list of sequences represented by their identifiers (UniProtAC or NCBI gi), if a cluster is already available. -
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A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees.
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Spaced Words Projection (SWeeP), is an application tool capable of generate phylogenetic trees from a large pool of sequences in a reasonably amount of time. It's the method implementation based on an alignment-free technique, capable of represent biological sequences using relatively small vectors while preserving inter-sequence comparability.
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SVPhylA
SVPhylA: Sequence Vectorization for Phylogenetic Analyses
SVPhylA is a python tool for the calculation of several alignment-free distances for phylogenetics analysis from the most popular alignment-free approaches. Such alignment-free methods basically encode DNA and protein sequences (fasta files) into numerical vectors allowing the calculation of alignment-free distances which may be combined into a consensus/compromise matrix by using algorithms like DISTATIS based on Multidimensional Scaling (MSD), Lineal Principal Component Analysis (PCA) and... -
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TI2BioP allows mainly the calculation of topological indices (spectral moments) derived from inferred and artificial 2D structures of DNA, RNA and proteins being possible to carry out a structure-function correlation irrespective of sequence alignments. TI2BioP version 3.0 is a python platform with a graphical interface designed for Windows, Linux and Mac OS.
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RELEASE NOTE: Get raxmlGUI 2.0 at the NEW PROJECT LOCATION: https://antonellilab.github.io/raxmlGUI/ raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. A userfriendly graphical front-end for phylogenetic analyses using RAxML (Stamatakis, 2006). Please cite: Silvestro, Michalak (2012) - raxmlGUI: a graphical front-end for RAxML. Organisms Diversity and Evolution 12, 335-337. DOI: 10.1007/s13127-011-0056-0
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The SPInDel workbench is a computational platform to facilitate the planning and management of SPInDel projects, alignment of nucleotide sequences, visualization and selection of conserved regions, calculation of PCR primers properties, prediction of SPInDel profiles and diverse statistical and phylogenetic analyses. It includes a large dataset comprising nearly 1,800 numeric profiles for the identification of eukaryotic, prokaryotic and viral species.
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Weinberg-CMfinder
Predict and score RNA secondary structures
... (2) other tools score alignments to indicate evidence of RNA secondary structure within the alignment. RNAphylo assigns a probabilistic score to an existing alignment, using an explicit phylogenetic model. hmmpair assigns a score based on evidence of covariation that is supported by sequence conservation. The ScoreMotif.pl script combines these two scores into one. CMfinder 0.4.1 was written by Zasha Weinberg, based on the CMfinder 0.3 package by Zizhen Yao, Infernal 1.1 by Eric Nawrocki and Sean Eddy, and others. The main differences of CMfinder 0.4.1 are handling truncated metagenomic sequences, integration of infernal 1.1 and the hmmpair program. ... -
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SUNPLIN
SUNPLIN: Simulation with UNcertainty for PhyLogenetic INvestigations
SUNPLIN: Simulation with UNcertainty for PhyLogenetic INvestigations -
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idwtree
Assigns orthologs using a phylogenetic tree
...with CLUSTAL OMEGA or MAFFT). 4. Use the alignment to build a phylogenetic tree (e.g. with the PHYLIP package) 5. Use idwtree to assign BLAST hits to ortholog groups -
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CoreAlyze
Use core genes to assess the coverage and fragmentation of a gene set
...The characteristics of this subset provide insight into the coverage and fragmentation of the input gene set as a whole. CoreAlyze places its findings in context with other gene sets, adding to the robustness of the results. CoreAlyze also provides phylogenetic and biological information about input genomes. -
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Evolutionary relationship of species provides a great deal of information about their biochemical machinery. So many researchers focus on the research of constructing the phylogenetic tree. A phylogenetic tree is a representation of evolution, tree normally describe the evolution of the species where the sequence are found.A method called the neighbor-joining method is proposed for constructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a star like tree. ...
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microbiome profiling
taxonomic profiling of microbiome
Microbial communities are responsible for a broad spectrum of biological activities carried out in virtually all natural environments including oceans, soil and human-associated habitats. Profiling the taxonomic and phylogenetic compositions of such communities is very important. A major goal of metagenomics is to characterize the microbial diversity of an environment. The most popular approach relies on 16S rRNA sequencing. Metagenomics combined with 16S rRNA gene sequence analyses was applied to unveil the taxonomic composition and functional diversity of the required microbiome. ... -
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AccNET
AccNET: Accessory Genome Constellation Network.
AccNET is a Perl application that presents a new way to study the accessory genome of a given set of organisms. Using the proteomes of these organisms, AccNET create a bipartite network compatible with common network analysis platforms. AccNET collects phylogenetic and functional information in a network improving the analysis capability. Networks offer a new perspective of organism organization through elements acquired by horizontal gene transfers and not constricted by hierarchical structures. AccNET has moved to GitHub Repository: https://github.com/valflanza/accnet -
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sophi
Structurally-Optimized-PHylo-Informatics
SOPHI (Structurally-Optimized-PHylo-Informatics). Linux phyloinformatics pipeline. Optimized for key informational partitions in public DNA sequence data. Enables upwards scaling of phylogenetic trees. -
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Community profiling (CP) is a guilt-by-association approach for predicting functional associations between proteins: two proteins are predicted to be associated if they share similar presence and absence profiles (called community profiles) across microbial communities. Community profiling is conceptually similar to the phylogenetic profiling approach to functional prediction, however with fundamental differences. This package provides different profile construction methods and correlation metrics, which we have shown are important for optimizing the performance of this new approach. Please refer to our paper for details of the algorithm: Dazhi Jiao, Wontack Han and Yuzhen Ye. ...
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hakmer
Parses genome sequences into k-mers for phylogeny reconstruction
...The code relies on a new implementation of suffix arrays to store and retrieve orthologous k-mers across several genomes. Resulting k-mer blocks can then be combined into one or more supermatrices for further phylogenetic analysis. -
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PhyloPart
automated partition of phylogenetic trees
Understanding the determinants of virus transmission is a fundamental step for effective design of screening and intervention strategies to control viral epidemics. Phylogenetic analysis can be a valid approach for the identification of transmission chains, and very-large data sets can be analysed through parallel computation. Here we propose and validate a new methodology for the partition of large-scale phylogenies and the inference of transmission clusters. This approach, on the basis of a depth-first search algorithm, conjugates the evaluation of node reliability, tree topology and patristic distance analysis. -
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metawatt
Binner for assembled metagenomes
The Metawatt binner is a graphical binning tool that makes use of multivariate statistics of tetranucleotide frequencies and differential coverage based binning. It also performs taxonomic assessment of binning quality (via diamond BLASTx). Created bins can be edited and exported as fasta. The Metawatt is implemented in Java SWING and minimally depends on Diamond, HMMer3.1, BBMap, Prodigal and the Batik library for the export of SVG graphics. Citation: Strous M, Kraft B, Bisdorf R,...
