Biostar

985 results • Page 1 of 20

Hi there, Crosspost to the google group for ETE3: I'm trying to install etetoolkit (http://etetoolkit.org/) via conda on MacOS and keep getting the same error. Google has been...and reinstalled miniconda. As suggested on the website, I ran the following: conda create -n ete3 python=3 conda activate ete3 conda install -c etetoolkit ete3 ete_toolchain Then I get the following er…

etetoolkit conda ete

updated 2.9 years ago • courtney.stairs

Hi, I recently installed [ete][1] via conda, so have a new environment for ete. I was able to use it to generate trees using ete3 build -w standard_raxml -a NUP62.aa.fa...Slr (3 CPUs) Traceback (most recent call last): File "/pub38/kayussky/anaconda3/envs/ete/bin/ete3", line 11, in load_entry_point('ete3==3.1.1', 'console_scripts', 'ete3')() File "/pub38/kayussky/ana…

ete paml ete3

updated 6.2 years ago • Kay

Hi, I'm having some trouble installing ete3 using the recommended conda way. I first ran `conda install -y pip six numpy pyqt lxml gcc` to install all the dependencies...but then when I ran `conda install -c etetoolkit ete3 ete3_external_apps` I was met with this error: UnsatisfiableError: The following specifications were found

conda ete3

updated 4.6 years ago • jyu429

Any idea why ETE Toolkit (ete3) throws an error while parsing the following Newick tree: > ((((A,B),C),(((D,E),F),(((((G,H),I),J),K),L)))(M,N)); from ete3 import Tree s = '((((A,B),C),(((D,E

ete3 newick tree ete

updated 5.2 years ago • a.zielezinski

I'm using ete toolkit to get a phylogenetic tree for a list of ncbi taxids: ```py from ete2 import NCBITaxa ncbi = NCBITaxa() tree = ncbi.get_topology

tree python ete

updated 2.2 years ago • whooli

I am wondering it the trees obtained by MrBayes can be viewed by ete2. Currently I am using FigTree. Thanks

python biopython

updated 10.8 years ago • Pappu

I have one command to grep the family information from the species data. cut -f1 species.txt | ete3 ncbiquery -info Can anyone please explain me whats then problem in this command. I am getting some error. Auroshis Mahakud...15:12 (0 minutes ago) to me usage: ete3 [-h] {mod,extract,annotate,compare,view,ncbiquery,generate,evol,maptrees,build,version,upgrade-external-tools} …

family information

updated 2.8 years ago • AUROSHIS

Is there a way to create an ultrametric tree in ETE (preferably ete2) for a tree that contains some internal branch attribute labels. I can make one with no attributes set, however

python phylogenetics

updated 8.4 years ago • moranr

Is there a way to do an ete3 type of analysis to get duplication events in R? I'm specifically looking for equivalents of reconcile() and .get_descendant_evol_events...Is there a way to do an ete3 type of analysis to get duplication events in R? I'm specifically looking for equivalents of reconcile() and .get_descendant_evol_events() So far, I've been working with ggtree but I kinda got stuck an…

ete3 bioconductor r ggtree python

updated 24 months ago • Alice

there is of course no "ARA" and "THE" species in the tree. Thank you! The whole code is: ``` from ete2 import PhyloTree, TreeStyle alg = """ >SOLTU_M1A5X1 MASRRLIASLLRSSAQRGAGSGGGPISRSSIANSIARPASRASPKGFLLNRAVQYATSAAAPASKPS...tree_style=ts) #recon_tree.render("phylotree.png", w=750) ``` [1]: http://pythonhosted.org/ete2/tutorial/tutorial_phylogeny.html#id4

ete python phylogeny ete2

updated 3.1 years ago • droidlove

Hello, I am using ete3 build to build a phylogeny of my target species. I ran the following command: ete3 build -a eteinput.faa --cogs outfile.tab...following error: Traceback (most recent call last): File "/home/nitin/anaconda3/envs/ete3/bin/ete3_apps/bin/pmodeltest.py", line 582, in <module> main() File "/home/nitin/anaconda3/envs/ete3/bin/ete3_apps/bin/…

ete3 ete3toolkit ete phyml

updated 18 months ago • nitinra

Hi! Does anyone know where ete3 evol stores the results of the likelihood ratio test (LRT), specifically the p-value? I can see the results on the command...anywhere (specifically the p-value of the LRT test). Here is the command i'm using to run it: ete3 evol -t tree.nw --alg tree_used_alg.fa -o results/ --models M1 M2 --image figure.pdf Thanks

paml LRT ete3

updated 3.3 years ago • mnsp088

Hi there, I am trying to load a treefile with ete3 using the following: from ete3 import Tree t=Tree("ROOT_LGM60.treefile") However, when I do this, I get the following error...t=Tree('ROOT_LGM60.treefile', format=0) File "C:\Users\kelse\Anaconda3\lib\site-packages\ete3\coretype\tree.py", line 213, in __init__ quoted_names=quoted_node_names) File "C:\Users\kelse\Ana…

etetoolkit

updated 2.8 years ago • k.williamson

Hi, How can I change the line width in ete3 phylogeny tree plotting? Thanks

ete3 phylogeny tree

updated 8.1 years ago • bluebug

The first **beta** version of ETE-NPR, a software for Nested Phylogenetic Reconstruction (NPR, related: https://peerj.com/preprints/223/) and workflow design...problem, comment or feedback. Stay tuned for upcoming changes and new releases*: http://twitter.com/etetoolkit [1]: http://etetoolkit.org/ete_npr

phylogenetics super-matrix gene-tree ete2

updated 3.2 years ago • jhc

Hi all, I'm running ete3 evol to detect positive selection in a list of orthologs. I realized something strange, I get different results if I run...should be independent of each other. Here is my code: for i in $(ls); do cd $i echo $i ete3 evol -t clustalo_default-none-none-fasttree_full/$i.fa.final_tree.nw --alg clustalo_default-none-none-fasttree_full

selection ete3 paml

updated 3.1 years ago • mnsp088

Good evening @all, I need help on how to parse lists of species list to ETE3 Toolkit. I have like 1000 CDS which I need to build a phylogenetic tree for, each file contains a varied number of species...tree with the name of the text_file. I have been stuck at this point: #!/usr/python3 import ete3 from ete3 import Tree import os import glob from pathlib import Path …

ETE3 Python

updated 3.7 years ago • Enhancer

Does anyone know how to prevent the `ete3` toolkit `compare` tool from truncating names in it's output? e.g. `ete3 compare -r /path/to/my_reference_tree_with_a_really_long_name.nwk

congruency comparison phylogenetics trees

updated 6.7 years ago • Joe

Hi all, does anyone know how to check if a tree has been correctly converted to ultrametric with ete3 in python? Kinda like the is.ultrametric() function of the R ape package? Thanks

phylogeny python

updated 6.9 years ago • Selenocysteine

From version 2.3+, [The ETE toolkit][1] provides a set of command line [tools][1] to perform a variety of tree-related operations (i.e. tree building, tree...etetoolkit.org/static/img/etebuild_screen1.png" style="height:326px; width:250px"/> ][7] Check [ETE-build in action][8] Notes: - At the moment, ETE build is prepared to run only on Linux-based platforms. - ETE-build uses many extern…

phylogeny etetoolkit alignment tree sequence

updated 2.2 years ago • jhc

I'm trying to collapse leaves that have the same name in ETE3's tree. I think I almost got it. Two leaves in my example (`A. thaliana`) have been combined into a single leaf, but not named. I would...like it to have the same name as its components. ```py from ete3 import Tree def collapsed_leaf(node): if len(node2labels[node]) == 1: return True else: return False t1 = Tre…

python ete3

updated 11 months ago • Andrzej Zielezinski

Hello, I'm trying to using ete3's ncbitaxa to get species-to-genus taxid's. I noticed that there are some taxid that aren't found (e.g.1913078 or 1283312

ete3 python ncbiTaxa taxonomyid

updated 6.5 years ago • bitpir

Hi everyone, I am working with ETE3 and I stumbled upon an error that I have never retrieved before: ete3.coretype.tree.TreeError: 'Nodes are not connected...seems to trace back to the `get_common_ancestor()` function, which is in the `tree.py` script of ETE3. The lines raising the error are these, within a `prune()` command: IDs_to_keep = [ ID for ID in Relevant_ID_list ] ... …

ETE phylome phylogenetics nodes TreeError

updated 6.0 years ago • Macspider

I have built a tree in Python using ETE3 package. Now I need to convert to extended Newick format, ideally using the same package. Can anybody help me out

ete3 Newick python

updated 22 months ago • hazelle64

Hi, Is there any way to force the tree to look like a cladogram in ETE? I can make the tree I want , but now I just want to add the style of the tree to have aligned branches the terminate at the same

python ete

updated 2.4 years ago • moranr

also a function that will translate the species name to taxonomy ID. Both functions are found under ETE3 I don't know what values/variables would go in the functions(at the end of the list) to get a result. My current code in python...Studio Code) after activating anaconda is ```py import pandas as pd import numpy as np import ete3 ``` pip install ncbi-taxonomist Which gives Note: you ma…

etetoolkit

updated 19 months ago • Gino

pub/taxonomy/ I found an excellent library on python called http://etetoolkit.org/ Ete3 can load NCBI taxonomy with this command: ncbiTaxa = NCBITaxa(taxdump_file=path.abspath(localTaxdumpArchive)) Is it

taxonomy taxdump ncbi ete3 toolkit

updated 3.8 years ago • Pierre

0.02140582)0.859000:0.03020852)0.978000:0.07396867); ``` I am trying to read it using: ``` from ete3 import Tree t = Tree(tree) ``` I have got an error: > ete3.parser.newick.NewickError: Unexisting tree file or Malformed newick

ete3 newick

updated 2.0 years ago • Jimpix

I am trying to parse a Newick file downloaded from the [Open Tree of Life][1] server using the ete3 python package: from ete3 import Tree tree = Tree('Vertebrata.tre', format=1) and getting the following error: raise NewickError

newick python ete3

updated 2.8 years ago • liorglic

Hello, I am a long time python ete3 user and have yet to encounter the following error message when calling t.render(). ![enter image description here][1] I believe...without the motifs although I need to render the motifs along with the tree for publication (citing ete3). Another consideration was the number of records, however I have constructed figures with even more records (and i…

SVG phylogenetics etetoolkit

updated 3.4 years ago • bdighera

Hi, I would like to start using ETE Toolkit (http://etetoolkit.org/) for creating a phylogenetic tree from DNA sequences from severla human individuals. I...Hi, I would like to start using ETE Toolkit (http://etetoolkit.org/) for creating a phylogenetic tree from DNA sequences from severla human individuals. I already...to specify and know the topology of the tree beforehand. Is there a way to …

phylogenetic tree ete3

updated 7.8 years ago • jyu429

I have a list of species from which I would like to generate a collapsed binary newick tree. I have tried in ete3, but it does not work. (PhyloT has this feature, but cannot be used as it is not free anymore ) ex) poly_1 = Test_tree.get_common_ancestor("Larimichthys crocea - 215358", "Takifugu rubripes - 31033") print(poly_1) poly_2 = poly_1.resolve_polytomy(recursive=True) prin…

ete3 Phylogenetics Python PhyloT

updated 5.5 years ago • View7

Hi, I want to print a tree with selected attributes using ete3 in python using a Newick (with NHX annotations) file e.g. : (dog[&&NHX:Genes=3:Identical=3:Duplicated=0:Lost=0:Novel=0:Singleton

python ete phylogenetics ete3

updated 2.4 years ago • moranr

Is there a way to add attributes to the SVG output of the ETE tree drawing toolkit? I am drawing phylogenetic trees as svg and would like to add the NCBI taxonomy ID as ID attribute...Is there a way to add attributes to the SVG output of the ETE tree drawing toolkit? I am drawing phylogenetic trees as svg and would like to add the NCBI taxonomy ID as ID attribute to

svg etetoolkit phylogenetic-tree

updated 2.2 years ago • lelle

Hi, I know ETE3 has a bunch of useful functions that deal with NCBI Taxonomy. But is there a way to list NCBI taxonomy identifiers of all

NCBI ETE3 taxonomy

updated 2.9 years ago • a.zielezinski

Hi everyone, I'm trying to apply some site models to detect positive selection in proteins using [ete3 evol][1]. After a lot of troubleshooting, I realized it requires a 'codon based alignment'. I currently just have a list of protein...based alignment'. Has anyone had this issue before? [1]: http://etetoolkit.org/documentation/ete-evol/ Thanks

paml slr alignment codeml ete

updated 3.3 years ago • mnsp088

how can I color the phylogenetic tree based on leaf name by using this text file with the help of ete3 ? Thanks in advance

sequence

updated 5.5 years ago • shiv

Anybody has a simple R script for Fst (Reynolds et al. 1983). thanks

fst population genetics snp

updated 12.5 years ago • user

to export my output trees in a different format like Newick, or one that is fully compatible with ETE 3 and other programs used to visualize trees

phylogenies Paup trees

updated 8.3 years ago • joreamayarom

order_id family_id genus_id species_id I am using the package "[ete3][1]". I use the tool [ete-ncbiquery][2] that tells you the lineage from the ids above. (I run it from my linux laptop with the command...below) ete3 ncbiquery --search 1204725 2162 13000163 420247 --info The result looks like this: # Taxid Sci.Name Rank Named Lineage Taxid...am looking for…

phylogenetics taxonomy

updated 8.1 years ago • crespialba

gt; "*An enterotype classification model, fit on 278 MetaHIT samples (E. > Le Chatelier et al., 2013)*" In the [De Costea et al., 2018 publication][2] associated to the online classification model, it's also referring to &gt...278 MetaHIT samples [3]*", where [ref \[6\] = E. Le Chatelier et > al., 2013][4]. **I'm looking for the FASTQ corresponding to those 278 samples.** …

Enterotypes MGnify

updated 21 months ago • erwan.scaon

I need to store all of the resulting trees as newick files. I was wondering if that is possible with ete or any other python related library. Thank you very much

Python

updated 7.8 years ago • mavino

I was wondering if anyone knew how Dobin et al. mined the plotted information in Figure 3 in the STAR paper? These include Number of unannotated junctions, % of mapper

RNA-Seq STAR Figures

updated 5.9 years ago • helen

containing a value inside the feature `feat`. I tried to use the collapsing functions used in the ETE2 documentation, but they don't seem to work well and they produce a non-complete newick tree which is not readable by the...ete2 module (or maybe I did something wrong). Can someone tell me how to do that

python ete2

updated 3.2 years ago • Abdullah

groups (HOG) stored in OrthoXML files I need to use the Pyham application which requires the ETE toolkit. I have a linux computer and I work using the command line, but I am new using python and I have not found a way to follow...the instructions to follow from the start? I have already installed Python 3.5.2 Qt 5.7.0 PyQT ete3 conda "The first step is to instantiate a pyham.taxonomy.Taxonom…

Pyham HOGs orthoxml

updated 6.1 years ago • dtejadamartinez

I am trying to visualize the tree using ete2 and figtree. But the programs don't seem to understand the bootstrap value given in `RAxML_bipartitionsBranchLabels.test

ete2 figtree raxml bootstrap

updated 2.8 years ago • Pappu

Hi, I have the Behar et al (2010) data set from GEO which is in Illumina's TOP/BOT format. It is a series matrix downloaded from GEO. They used this [platform

next-gen illumina SNP Population-Genetics PLINK

updated 2.3 years ago • aritra90

Could someone explain how Garrison et al. simulated the sequence reads used to evaluate vg in [their paper][1]? Maybe I'm missing something obvious, but I don't see the

updated 4.2 years ago • ac2278

tree using seaview. Recently I realized that the tree rendering is inaccurate and differs from MEGA, ete2 and ITOL. Let me know if you have similar experience with seaview. Thanks

updated 11.5 years ago • Pappu

I downloaded the ChIA-PET data from https://www.ncbi.nlm.nih.gov/sra/SRX1210752 which was provided by "CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Tang et al. Cell, 2015, 163(7): 1611-1627.". The authors claimed that DNA products were then subjected to size-selection and paired-end sequencing...by "CTCF-Mediated Human 3D Genome Architecture Reveals …

ChIA-PET

updated 7.5 years ago • caochch

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