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Showing top results for tag: phylogenetics • reset
11
votes
17
replies
1.5k
views
6 follow
Interpreting phylogenetics tree
phylogenetic-tree itol phylogenetics
updated 5 weeks ago by 44k • written 7 weeks ago by ▴ 50
4
votes
2
replies
311
views
GGTree flips my trees
R ggtree phylogenetics
8 weeks ago by M. ▴ 40
0
votes
0
replies
179
views
Tool: Phylogenetic Tree Collapser
phylogenetics
3 months ago by Hugo ▴ 380
0
votes
0
replies
193
views
ABBA-BABA Analysis for Identifying Ancestral Contributors in Plant Species Evolution
OrthoFinder D-suite ABBA-BABA Phylogenetics
4 months ago by alexis.groppi ▴ 40
1
vote
3
replies
1.0k
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics bootstrap
updated 5 months ago by ▴ 160 • written 6 months ago by ▴ 40
0
votes
0
replies
196
views
How to get the minimun branch distance tree?
distance tree phylogenetics
7 months ago by Destineador • 0
0
votes
0
replies
411
views
r8s error in cross-validation step
r8s divergence rate time evolutionary phylogenetics
12 months ago by Simone ▴ 10
3
votes
6
replies
1.4k
views
GGtree flips my tree
ggtree phylogenetics R
updated 8 weeks ago by 44k • written 15 months ago by ▴ 40
0
votes
0
replies
472
views
Divergence dates change when pruning chronogram
evolution R ape chronogram phylogenetics
15 months ago by Morgan S. ▴ 90
0
votes
1
reply
486
views
Measuring Evolutionary Distance Between Species from Chronogram
phylogenetics
updated 15 months ago by ★ 1.1k • written 15 months ago by ▴ 10
0
votes
2
replies
1.1k
views
Extract Divergence Times and Corresponding Node Numbers from a Time Tree
phylogeny R ape phytools phylogenetics
13 months ago by Simone ▴ 10
0
votes
3
replies
4.0k
views
10 follow
Forum: Discussion question: Cutoff for SNP phylogeny
Phylogenetics SNP
written 23 months ago by ▴ 130
2
votes
2
replies
741
views
Phylogenetic tree visualization
ete3 phylogenetics
15 months ago by M. ▴ 40
0
votes
0
replies
454
views
Weird (very large) values for branch lengths in BEAST MCC trees?
beast analysis bayesian phylogenetic phylogenetics
16 months ago by clmattson • 0
0
votes
0
replies
726
views
Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average.
translation codon phylogenetics
updated 16 months ago by 44k • written 16 months ago by ▴ 10
0
votes
0
replies
676
views
Automatically construct a genus-level data matrix using sequences from GEBANK, for phylogenetic analyses
GENBANK RAxXML NCBI phylogenetics
16 months ago by lychen83 • 0
3
votes
5
replies
1.8k
views
seqboot ERROR: sequences out of alignment (SOLVED)
alignment sequence protein bootstrap phylogenetics
updated 16 months ago by 85k • written 16 months ago by ▴ 20
1
vote
0
replies
1.1k
views
Job: Postdoctoral position in Evolutionary Structural Bioinformatics
urmetazoan OMA phylogenetics common-ancestor
updated 16 months ago by 44k • written 16 months ago by ▴ 20
3
votes
2
replies
1.2k
views
Modeltest-ng and MrBayes
Modeltest model phylogenetics Mrbayes selection
16 months ago by Francisco Pina Martins • 0
0
votes
0
replies
512
views
News: Course - Phylogenetic Comparative Methods in R
Comparative-Methods R Phylogenetics
updated 17 months ago by 44k • written 18 months ago by ★ 2.6k
0
votes
0
replies
337
views
What is the limit of partition incompleteness?
beast mcmc phylogenetics bayesian
18 months ago by Mordovian Guy • 0
0
votes
1
reply
587
views
How do I shift the edge length of multiple trees in R?
phylogenetics edge-length R
updated 18 months ago by 44k • written 18 months ago by • 0
0
votes
5
replies
1.0k
views
Find corresponding branch from gene tree in species tree
phylogeny family-tree gene species phylogenetics
updated 21 months ago by 3.8k • written 21 months ago by ▴ 70
4
votes
2
replies
1.6k
views
Advice on publishing maximum likelihood trees
sequencing phylogenetics maximum-likelihood
updated 21 months ago by 44k • written 5.5 years ago by ▴ 80
3
votes
3
replies
1.3k
views
Phylogeny inference on complete chloroplast genomes with IQ-TREE software
IQ-TREE genomics phylogenetics
updated 21 months ago by ★ 1.4k • written 21 months ago by ▴ 310
2
votes
1
reply
569
views
Example of Phylogenetic Tree Construction by MLE?
mle phylogeny genomics sequencing phylogenetics
updated 23 months ago by 4.9k • written 23 months ago by ▴ 30
3
votes
2
replies
2.0k
views
MrBayes - big difference in average standard deviation of split frequencies between CPU and GPU versions
GPU phylogenetics MrBayes
23 months ago by wstfljs ▴ 100
1
vote
2
replies
646
views
Can you do a sequence alignment with an uneven number of genes? (For phylogenetics)
alignment phylogenetics sequence
updated 24 months ago by 146k • written 24 months ago by ▴ 30
0
votes
1
reply
496
views
How to retrieve all genes of interest from GenBank?
ncbi genbank phylogenetics mitochondria
updated 24 months ago by 101k • written 24 months ago by ▴ 30
0
votes
0
replies
426
views
Is it normal for maximum likelihood estimation to take too long?
ML phylogenetics tree
2.0 years ago by hojoun • 0
5
votes
2
replies
3.3k
views
dN/dS in a tree (multiple genes)
dN/dS dNdS KaKs Phylogenetics PAML
23 months ago by BlastedBadger ▴ 160
5
votes
1
reply
530
views
Conceptual phylogenetics questions
LBA Phylogenetics
updated 2.1 years ago by ▴ 460 • written 2.1 years ago by • 0
3
votes
4
replies
1.0k
views
Should assemblies be removed if core gene alignment is identical?
phylogenetics genome alignment pangenome
2.1 years ago by c_u ▴ 520
4
votes
1
reply
686
views
assembly based phylogeny
whole-genome phylogenetics assembly
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by ▴ 580
0
votes
3
replies
749
views
Construct a phylogenetic tree of apes
phylogenetics msa
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by ▴ 40
1
vote
4
replies
1.4k
views
Trouble Running MrBayes with GPU(s)
phylogenetics MrBayes Bayesian GPU inference
updated 2.2 years ago by ★ 28k • written 2.2 years ago by • 0
1
vote
0
replies
327
views
r package for downstream analysis of phylogenetic trees
phylogenetics R
2.2 years ago by TM ▴ 10
6
votes
1
reply
3.5k
views
snp phylogenetics vcf to tree
SNP phylogenetics vcf
updated 2.4 years ago by • 0 • written 7.6 years ago by ▴ 130
0
votes
3
replies
862
views
What does the LJ.8 mean in "Capra hircus isolate LJ.8 beta-casein (CSN2) mRNA, complete cds"?
phylogenetics ncbi mega
updated 2.5 years ago by ▴ 930 • written 2.7 years ago by • 0
0
votes
0
replies
403
views
Missing ',' in line when Biopython reads a nexus tree
biopython nexus phylogenetics
2.6 years ago by Mordovian Guy • 0
2
votes
2
replies
945
views
Help with phylogenomics
iqtree Phylogenetics Time-tree evolution Mega
2.6 years ago by Space_Life ▴ 50
0
votes
0
replies
334
views
Phylogenetic tree to splits matrix
python R phylogenetics
2.6 years ago by DR ▴ 10
0
votes
0
replies
703
views
BEAGLE do not see and/or not use OpenCL
phylogenetics BEAST2 BEAGLE
updated 23 months ago by 44k • written 2.6 years ago by • 0
0
votes
0
replies
387
views
Problems with using GEO_SPHERE package in BEAST 2
phylogeography phylogenetics BEAST2
updated 23 months ago by 44k • written 2.7 years ago by • 0
0
votes
0
replies
554
views
ggtree collapsed clade+images
ggtree plotting R phylogenetics
2.7 years ago by Gabriel R. ★ 2.9k
3
votes
2
replies
795
views
Conflict between MAFFT and new PRANK installation
multiple-sequence-alignment bash prank mafft phylogenetics
updated 13 months ago by 44k • written 2.7 years ago by • 0
0
votes
0
replies
330
views
Unrooted trees useless and can mean anything?
msa Phylogenetics
2.7 years ago by Platelet Guardian • 0
2
votes
1
reply
585
views
iTOL phylogenetic tree visualization
Phylogenetics
updated 21 months ago by 44k • written 2.7 years ago by ▴ 30
3
votes
3
replies
1.8k
views
What does it mean when a FASTA file has many "NNN's"?
fasta phylogenetics mega
updated 2.7 years ago by ▴ 350 • written 2.7 years ago by • 0
4
votes
6
replies
1.2k
views
How to get gene sequences from non-model species for phylogenetic tree construction?
yeast blast annotation phylogenetics
updated 2.8 years ago by ▴ 110 • written 2.8 years ago by ▴ 50
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Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type by conmul • 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
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Thank you for your answer, it's very inspiring.
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Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
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Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
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The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
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I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
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What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
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The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
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Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
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The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
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any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
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What p-value do you mean? When and how did you calculate it?
Answer: What is a genomic range that would almost always get decent WGS coverage but is by i.sudbery 20k
What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
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One of the improvements that the using the `salmon` -> `tximport` -> `DESeq2` pipeline, over just a `counts`->`DESeq2` pipeline is the abil…
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