Biostar

963 results • Page 2 of 20

concordance factors as support values. I have checked the documentation of iqtree, toytree and ete, but cant find a solution. The actual tree file looks like this: (MjavVW4_2:0.0037628199,((MincW1_2:0.0034335950,MfloSJF1_2

iqtree phylogenetics concordance factors newick

updated 3.8 years ago • mrmrwinter

that are made that I am missing? Is there a separate power test other than the one proposed in [Skol et al. (2006)][3]? Thanks! [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/instance/2694957/bin/nihms106702f2.jpg [2]: http://csg.sph.umich.edu

genome

updated 4.0 years ago • aakashi

be able to make a FASTA available for the following draft assemblies reported in the 2015 Paulino et al. BMC Genomics article? *E. coli* *S. cerevisiae* *C. elegans* *H. sapiens* *P. gluca* I look forward to getting abyss-sealer running in

abyss

updated 21 months ago • jshelton

Hi, I would like to get a taxonomic tree with a list of taxids.. I've tried get_topology from ete3 package, but the tree returned is in an illustrative format.. I would like to have a string representation, something like

ete tree

updated 3.4 years ago • raquelle70679

Hello all, I'm trying to use the [Hi-C data][1] provided by Bonev et al. in their 2017 paper, which are in the form of binaries. The authors used a tool called [shaman][2], which requires a [misha][3] database

R genome Hi-C

updated 5.1 years ago • elyk_bear

line 9, in t = Tree("contents") File "/usr/local/lib/python2.7/dist-packages/ete3/coretype/tree.py", line 211, in __init__ quoted_names=quoted_node_names) File "/usr/local/lib/python2.7/dist-packages...ete3/parser/newick.py", line 249, in read_newick raise NewickError('Unexisting tree file or Malformed newick tree structure...since I have my file in correct format. I …

Python Newick Format Import files

updated 6.2 years ago • ArusjakGevorgyan

I am trying to color the backgroud of a bubble tree using ETE2 in python. However I am not sure how to color the background like this: http://ete.cgenomics.org/ I can color the background

python

updated 10.1 years ago • Pappu

leaves. I would like to convert these numbers into species names. I already tried to solve this with ete3 within Python or Archaeopteryx to download this information from NCBI. This did not work out. Would be great if someone

phylogeny archaeopteryx figtree ete3

updated 4.5 years ago • peterlageweg603

I am trying to download the van't Veer et al. (2002) breast cancer dataset using breastCancerNKI package on Bioconductor. This is my code library("breastCancerNKI

microarray breastcancer

updated 6.5 years ago • lur_murad

Hi, I'm stuck on how to convert a pairwise-distance matrix or phylim format into newick format. Newick format is the required input for plotting a tree for many programs yet there seems to me no straightforward method on how to build a newick file. ![phylip format][1] I'm gravitating towards using the Bio Phylo package however it cannot read phylim format so therefore can't convert it into new…

python phylogeny

updated 14 months ago • Linda

1)1:1)1:1)1:1);' ``` I want to get for each leaf node, a list of closely related leaf nodes using ete2 python. how can I do that

python ete2

updated 2.6 years ago • Abdullah

I'm trying to read my tree from the `classify/` directory from GTDB-Tk but I'm getting an error: In [50]: tree = ete3.Tree("./classify/gtdbtk.bac120.classify.tree", format=0, quoted_node_names=True) --------------------------------------------------------------------------- NewickError Traceback (most recent call last) in ----> 1 tree =…

metagenomics gtdb database phylogeny

updated 3.3 years ago • O.rka

Need to make a plot merging heat map and a phylogenetic tree in Python. I have already made the heat map using the square distance matrix that I have with the help of numpy and matplotlib but now I would like to merge a phylogentic tree with this heat map, For this purpose I found a BioPython Package called ETE2, however the problem with this is that it needs a newick formatted file instead of th…

python distance phylogenetics

updated 10.3 years ago • asmariyaz23

I am trying to replicate the analysis conducted in [Brennand et al][1] to cluster microarray expression data (or, in my case, RNA-seq data) with data available in the Allen Brain Atlas. I'm afraid

clustering R microarray RNA-Seq

updated 2.5 years ago • dvanic

with python? I already have the newick files for the trees and can process and plot them (e.g. with ete3 or Bio.Phylo), but I would love to get the x-y coordinates of those tree nodes and edges to generate interactive plots in

Dash python Plotly

updated 2.4 years ago • jon.winkelman

Spec2. Is it possible to do that with a simple script or does anybody knows a software (tried phybin, ete3 compare already). I will be grateful if you someone could help

tree clustering compare topology

updated 7.2 years ago • ibasan

Hi, I am trying to display attributes of a tree. The tree has been loaded in newick format with attributes (annotated in the newick file) e.g.: "Genes" , "Identical", "Duplicated" etc. When I try to make an image of the tree with these attributes I get an error. I am able to print the attributes and tree as ascii. ``` t=Tree('sampleGeneTree.tree', format=1) ts = TreeStyle() ts.show_leaf_name…

ete phylogenetics python

updated 2.6 years ago • moranr

H 6 6 6 6 6 6 6 0 1 I 6 6 6 6 6 6 6 1 0 I tried get_distance functions on ete3 but it does not give matrix based on node distance

tree distance matrix phylogeny

updated 4.2 years ago • Chvatil

What is the best codeml model to determine if a gene is undergoing positive, negative or neutral selection? At this point I am not interested in site specific omega values, but rather want to estimate a value for the whole gene. ete3 toolkit offers models from M0 all the way to M13. For the most part they seem to follow the same trend. I was wondering if M0...not interested in site specific omega…

codeml ete3 evol

updated 7 weeks ago • Adrian Pelin

be able to see how many XPA or other proteins are there for Intoshia linei. Can I do this with ete3? Or any other suggestions? Thanks in advance. [1]: /media/images/843bdb08-b956-4331-a2da-aa0bbd78

ete3 phylogenetics

updated 9 months ago • M.

Combined calling using GATK haplotyper SeqHBase: FamSeq (Peng et al. 2013): Triodenovo and PolyMutt (Li et al. 2012): MATE-CLEVER (Marschall et al. 2013): DeNovoGear: VariantMaster: Few more I might

famseq

updated 19 months ago • Rm

The edge manual I understand The classic edgeR approach is to make pairwise comparisons between the groups. For example, > et <- exactTest(y, pair=c("A","B")) will find genes differentially expressed (DE) in B vs A. Similarly > et <- exactTest(y, pair=c("A","C")) for C vs A, or > et <- exactTest(y, pair=c("C","B")) for B vs C. I have a query about…

edgeR

updated 2.6 years ago • Info.shi

Hi everyone, I wondering which bioinformatic tools / open source software are you missing, are outdated or difficult to use? I am looking for a side project as a software developer but want to implement something useful. Any feedback would be appreciated Cheers

software

updated 11 months ago • ete

Hi! Does anybody knows whether it's possible to set the output file name and location of the ViennaPackage tool rnaplfold? The default settings (sequence name and current directory) are not convenient. I am calling the tool via Python subprocess module. Any help would be very apprenticed, Thanks in advance! Stefanie

sequence

updated 18 months ago • ete

Hi, is it possible to get not only the position of the reference strand but also of the query sequence? I know it is possible to "find" the sequence on the query but that's a not so nice solution... Thanks

alignment

updated 21 months ago • ete

Hello! I am looking for beta testers for three bioinformatic tools I have written. They include a sequence alignment tool, a primer search and design tool and a small helper tool for the lab. If you are interested to test the programs (at the moment Windows only) please contact via labtools[at]ipk-gatersleben.de Best regards,

primer3 blast bowtie primer-design

updated 2.4 years ago • ete

Hello! I would like to advertise my new webpage and software tools (open source): http://www.snowformatics.com/ **Blaster **- A simple and intuitive multitool for performing some of the most common tasks in nucleotide and protein sequence work. **Primer Factory** - A primer design and primer search tool. **Labtools **- Common calculations in the lab. Any feedback, bug reports or features req…

primer blast alignment bowtie

updated 2.4 years ago • ete

Hello! I am using [RNAduplex][1] from Vienna package and trying to find out in which format the two sequences has to be passed to the cmd. The manual only say "reads two RNA sequences from stdin or ". I used a filename but this might lead to IOErrors if my query sequence is very long. Does anybody know how to give the two sequences? Thanks in advance! [1]: http://www.tbi.univie.ac.at/RNA/RN…

RNA-Seq

updated 2.5 years ago • ete

Hi, I converted my VCF file into plink binary formats by using plink2. As variant ID I need the following format (chrom_pos): chrom snp cm pos a0 a1 i 0 0 Chr1_657 0.0 657 T C 0 1 0 Chr5_1168 0.0 1168 G T 1 But I get only a point (.) chrom snp cm pos a0 a1 i …

vcf plink

updated 3.8 years ago • ete

Hello everybody! I'm planning to transform a few windows programs which I wrote into web applications. Can anybody give me some tips, suggestion or experience with this (Framework, Hosting)? I will use Python. I was thinking about GAE but unfortunately you can not run processes on it. I will need BLAST, Primer3 and Bowtie. Any help is appreciated! Stefanie

web python blast bowtie

updated 11.4 years ago • ete

not accept it. Do you have any simple way of making this work? ##gff-version 3 chrI Li et al. 2017 (maj TFW mars 2018) Gene 7295 16807 . + . ID=TrA0001W chrI Li et al. 2017 (maj TFW mars 2018) Gene 17180 19774 . - . ID=TrA0002C chrI...Li et al. 2017 (maj TFW mars 2018) Gene 20663 21727 . + . ID=TrA0003W chrI Li et al. 2017 (maj TFW mars 2018) Gene 22342 23250 . + . ID=Tr…

TSS GFF

updated 3.2 years ago • S.Fajon

On some of the suggestions here: https://www.biostars.org/p/230292/#230295 I'm taking a look at the ete3 toolkit and others, but I have a question: When comparing congruency with robinson-foulds, are branch lengths taken in

phylogenetics trees

updated 7.3 years ago • Joe

someone have an idea in order to add these informations by creating a `NHX format` in python (witg **ete3** for instance) or with a **R package** ? Here is the tree : Thank you for your help

newick nhx phylogeny python r

updated 3.2 years ago • Chvatil

Hi guys, My question is regarding the pipeline for identification of phasiRNAs in plants. There are many papers that have used an analysis method but were not very informative on how to execute the protocol. Links to papers: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457045/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867363/ http://link.springer.com/article/10.1007/s12042-016-9173-4 Me…

next-gen RNA-Seq

updated 5.5 years ago • v.baaskarla

Hi, in edgeR how can I write the FDR values to DE file? et <- exactTest(dgelist) fdr <- p.adjust(et$table$PValue, method="BH") I know exactTest doesnt produce FDR values but with fdr &lt...p.adjust(et$table$PValue, method="BH") i think i am calculating fdr values but how can I include them to DE file

edgeR rna-seq dge

updated 2.1 years ago • edus_bioinfo

damayanthi/sudu3/DTU-simulation/genome-data-sta --readFilesIn /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031718.fastq /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq...files/treated-1/SRR031719.fastq /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031720.fastq /media/damayanthi/sudu3/RQ2/brooks-et-al-data-anal…

STAR RNA-Seq Aligner

updated 6.3 years ago • damayanthikherath

Hi everyone, I ran PAML (via ete3 evol) to detect positive selection on two closely related strains of the same species (Species A and B in figure below...Hi everyone, I ran PAML (via ete3 evol) to detect positive selection on two closely related strains of the same species (Species A and B in figure below) and

ete3 paml

updated 2.4 years ago • jm440

Hello, I have a tree with duplication. I need to extract a subtree that is monophyletic to get orthologs. I have to following tree: t2 = PhyloTree("((RED_18455.t1:0.00147625,(YEL_2874.t1:0.0138986,YEL_23839.t1:0.0506878)n2:0.00563198)n1:0.000294125,BLU_7991.t1:0.00203445)n0;", format=1) print(t2) > /-RED_18455.t1 > /-| > | | /-YEL_2874.t1 > --|…

ETE3 python3

updated 3.2 years ago • arunprasanna83

d_from`, `d_to` and `d_step` to explore the distance cut-offs, X). You will need to install ete2 by simply executing these two bash commands if you have easy-install and Python: ``` apt-get install python-setuptools python...numpy python-qt4 python-scipy python-mysqldb python-lxml easy_install -U ete2 ``` [1]: http://meme.nbcr.net/meme/cgi-bin/dreme.cgi [2]: http://en.wikipedia.org/wiki/Newic…

promoter orthology gene-families DNA-motif

updated 2.3 years ago • a1ultima

Staphylococcus Staphylococcus epidermidis I got this result using the ktClassifyBLAST and [ete3][2], but for some taxids I got no information for some ranks, which do not occur in the krona chart. [1]: https://github.com/marbl

krona

updated 4.7 years ago • Diego Morais

for predicting protein protein interactions ? I've found some papers like Brohée & Helden, Yu et al., Tarassov et al., but which other papers would be worth taking a look at? Thanks

ppi

updated 9.7 years ago • Sudeep

does the following sentence mean? " The SNPs used were curated into the NHGRI GWAS catalog (Welter et al. (2014)) and obtained through the UCSC Table Browser (Karolchik et al. (2004)) on September 12, 2014." from: (http://egg2.wustl.edu

SNP GWAS

updated 7.2 years ago • mariamari693693

articles about 6-mA methylation prediction. I am very confuse why most of open data such as Chen et al. (Chen et al., 2019) and Lv. (6mA-RicePred) are in form of 41 bps long with the methylation label is at the center. Why they didn't collect

methylation 6mA

updated 19 months ago • Peter

Literature research resulted only in methods using sequencing based methods, such as RRBS ([Lee et al., 2019][1], [Barrett et al., 2017][2]; [Li et al., 2014][3]). Does anyone have an idea, whether such methods are also available for DNA methylation

methylation array clone tumor subclone

updated 3.9 years ago • ResearchR

has generated several large scale protein-protein interaction network (interactome; Mukhtar et al. SCIENCE, 2011; Arabidopsis Consortium, SCIENCE 2011; Klopffleisch et al. Molecular Systems Biology, 2011; Wesling et al...Cell Host Microbe, 2014; Smakowska, et al. 2018, NATURE) and transcriptional regulatory networks (Mishra et al, NPJ Systems Biology & Applications, Mishra et al...Scienti…

Networks data-analysis RNA-Seq

updated 11 months ago • bharat26oct

Hi, does anybody use DIALIGN-TX on OS X? We are [trying to get support][1] for it when using the "ete build" command to run phylogenetic workflows but, although it compiles well and seems to execute, it does not accept any...same command line runs ok under Linux. Any hint is appreciated! [1]: https://github.com/jhcepas/ete/issues/127

alignment phylogeny

updated 19 months ago • jhc

Dear group, Could anyone help, how Verhaak et al. used sigClust in their Cancer Cell paper. Verhaak et al used GBM expression matrix from TCGA (202 samples x 1740 genes). They...Dear group, Could anyone help, how Verhaak et al. used sigClust in their Cancer Cell paper. Verhaak et al used GBM expression matrix from TCGA (202 samples x 1740 genes). They obtained 4 clusters as meaningful using con…

sigclust R

updated 6.2 years ago • oriolebaltimore

is to correct the DNase cleavage bias, which has been extensively researched by his lab ([Lazarovici *et al., PNAS*, 2013][1]) and other labs ([Koohy *et al., Plos One*, 2013][2]; [He *et al., Nat Med*, 2014][3]; [Baek *et al., Cell Reports,* 2017][4]). As far as I know, packages...bias using the 6mer sequence frequency, because the DNase motif is 6bp. However, Lazarovici *et al.* reported th…

DNase-seq footprinting correction bias

updated 2.9 years ago • Hughie

driven research that aims developing algorithms for a wide range of applications (e.g. Yang et al., Bioinformatics 2010; Yang et al., BMC Genomics 2014; Yang et al., Genome Medicine 2015), to hypothesis-driven investigation...problems where the main goal is the discovery and advancement of biological knowledge (e.g. Asangani et al., Nature 2014; Henzler et al., Nature Communications 2016; Katernd…

cancer RNA genomics postdoc

updated 15 months ago • cauyrd