Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples

Background

Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical meth[……]

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fasta to nexus for beast

http://sequenceconversion.bugaco.com/converter/biology/sequences/fasta_to_nexus.php     […]

Data Binning and Plotting

In statistics, data binning is a way to categorize a number of continuous values into a smaller number of buckets (bins). Each bucket defines an numerical interval. For example, if there is a variable about house-based education levels which are measured by continuous values ranged between 0 and 19,[……]

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Histograms and Density Plots

Histograms and Density Plots

Histograms

You can create histograms with the function hist(x) where x is a numeric vector of values to be plotted. The option freq=FALSE plots probability densities instead of frequencies. The option breaks= controls the number of bins. # Simple Histogram hist(mtc[......]

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meta realted paper (转贴)

文章:Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes  2016 (https://www.ncbi.nlm.nih.gov/pubmed/27067514) 文章:MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression 2016 (http://w[……]

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ARGs-OAP: 抗性基因在线分析工具(转)

ARGs_OAP_v2.0(步骤1):https://github.com/biofuture/Ublastx_stageone ARGs-OAP在线分析网站(步骤2): http://smile.hku.hk/SARGs
无处不在的抗性基因

图片.png

环境中抗生素抗性基因(ARGs)的来源: 随机突变或表达潜在抗性基因等方式使细菌体内基因组上存在的抗性基因原型、准抗性基因或潜在抗性基因被表达出来,从而使细菌获得的抗生素抗性。 抗生素在人和动物肠道内诱导产生耐药菌,这些编码ARGs的耐药菌经由粪便排出并进入环境中,是环境中ARGs的重要来源。[……]

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tmap install

  1199 git clone https://github.com/GPZ-Bioinfo/tmap.git 1200 cd tmap 1201 ll 1202 python setup.py install 1203 ll 1204 cd ../ 1205 rm -rf tmap 1206 deactivate 1207 rmvirtualenv tmap_ENV 1208 mkvirtualenv -p /usr/bin/python3.4m tmap_ENV pip3 install pypiwin32 conda install sci[……]

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Basic Usage of tmap

import sklearn 
import plotly.plotly as py import plotly.graph_objs as go import matplotlib.pyplot as plt import numpy as np from sklearn.cluster import DBSCAN from sklearn import metrics from sklearn.datasets.samples_generator import make_blobs from sklearn.preprocessing import Stand[......]

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fasta2nexus by R script

Workspace loaded from ~/.RData] > setwd("/home/shenzy/work/beast/51samples") > library(seqinr) > data=read.fasta("51strain_core_gene_alignment.aln") > library(ape)  Attaching package: ‘ape’ The following objects are masked from ‘package:seqinr’: as.alignment, consensus[......]

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change the font size of leaf nodes when generating phylogenetic trees using Bio.Phylo.draw()

axes : matplotlib/pylab axes If a valid matplotlib.axes.Axes instance, the phylogram is plotted in that Axes. By default (None), a new figure is created.

This means that you can load your own axes with your size of choice. For example

import matplotlib import matplotlib.pyplot as plt from Bio im[......]

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