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Stars5
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Rank 2,847,076 (Top 57 %)
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LanguageShell
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Created almost 6 years ago
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Updated 5 months ago
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Repository Details
Scripts for plasmidome analysis
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MICROSTORE_MetaT-MetaB_Monjot_2023
Workflow to reproduce analysis conduced in Monjot et al., 2023R
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AccNetPhylA
This Perl script AccNetPhylA (Accessory Constellation Network with Phylogenetic Analysis) takes up most of the analysis of AccNET (Accessory Constellation Network) (Val F. Lanza et al., 2016) by replacing the clustering tool kClust (Hauser et al., 2013) with CD-HIT (Weizhong Li et al., 2001) for analysis with nucleotide and protein sequences. "AccNET is a comparative genomic tool for accessory genome analysis using bipartite networks. The software has been designed to be compatible with most of the Network Analysis software (i.e. Cytoscape, Gephi or R)."Perl
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MetaPathExplorer
MetaPathExplorer is a pipeline for analyzing and visualizing KEGG pathway maps (Kanehisa et al., 2002). These pathways are produced from high quality reads or contigs/scaffolds (metagenomes or SCs) or proteins.HTML
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HpC_to_vehicle
The perl script HpC_to_vehicle retrieves the results of the perl script AccNetPhylA (files to visualize the networks, multiple alignment of Muscle, phylogenetic results of PHYLIP, ...) to create HpC (Homologous protein Cluster) and GU (Genomic Unit), to thus make different networks representing the links between "vehicles" of genes or proteins. For each vehicle, there are two types of graphs: -network between vehicles that can belong to the same GU -network between different GU vehicles For gene vehicle analysis, a patristic distance (calculated from tree branch lengths describe the amount of genetic change represented by a tree) will be used to build two more graphs. In the end, there will be 4 networks resulting from an analysis with the genes and 2 from an analysis with the proteins.Prolog
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