phylobabble

This is an archived static version of the original phylobabble.org discussion site.

Topics Category Posts

Welcome to phylobabble.org! Uncategorized 3

Time to sunset the site? Meta 1

Criteria for deciding if concatenation of dna alignments to a supermatrix is “allowed” Sequences 13

What topics for FuturePhy hackathons? Events 7

25th annual New Zealand phylogenetics conference (Feb. 2021) Events 1

How much does ranking help? Topology 1

Generating a set of trees that are as different from each other as possible Topology 9

Indel models: Why continuous time? Sequences 3

Phylobayes: bpcomp and tracecomp help Troubleshooting 1

SARS-CoV-2 and COVID-19 Traits 1

Predicting the most likely location for a unknown discrete trait tip on the phylogeny Traits 2

Exporting ancestral reconstructions from PAUP* Software 3

Postdoc in Bioinformatics of HIV Los Alamos National Lab Positions 1

Several burning questions Sequences 5

Quantifying changes in clonal populations (phylo-epi) Dates 4

Molecular evolution of overlapping genes Uncategorized 3

Dating a virus evolutionary history Uncategorized 4

[Paper] An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics Software 1

A newbie question Troubleshooting 1

New software for supermtatrices of many genes/species Software 1

Course: Macroevolution on Phylogenies, Crete, July 16-19 Events 1

Stepping stone analysis given the difficult dataset Troubleshooting 3

PhD in Phylogenetic Inference of Pneumococcal Transmission Positions 1

Generalizing tree probability estimation via Bayesian networks Topology 1

Site should be fixed now after port 80 issue Uncategorized 1

Site-Specific amino acid selection presures Dates 1

PhD position: HPC for Phylogenetics Positions 1

Distances are important. Arthropods vs Mammals for example Sequences 1

Fast implementation of branch length likelihood gradients anywhere? Software 2

Cross-platform testsuite for phylogenetic likelihoods phyloinformatics 2

Postdoc position - joint between Chindelevitch and Bouchard labs Positions 1

Does defining outgroup a priori has effect on tree inference? Troubleshooting 4

[MrBayes] Weirid results in Tracer. Can someone help? Troubleshooting 5

Balanced minimum evolution computation in R Software 3

PhD scholarship with Semple/Steel on phylo-networks Positions 1

Split decomposition Software 3

Number of labeled histories given a topology? Topology 6

What are the compositional differences between Prokaryotes’ gene/genome and Eukaryotes gene/genome Sequences 2

Evolution/ESEB 2018 conference - abstract deadline: Jan 15 Events 1

IQ-TREE: Phylogenomic inference software Software 4

Interactive Phylogentic Tree Software 1

Postdocs in theoretical population genetics at the University of Chicago Positions 1

Looking for a zoomable tree to interface with mySQL for selection Software 2

Speeding up Felsenstein’s pruning algorithm Software 7

Any one who has good strategy to print a super-tree into separated-page pdf file Practicalities 18

The forum is on HTTPS now Uncategorized 1

Want to chair a JSM session? Events 2

Diversification rates and sampling fraction Uncategorized 4

“Online” algorithm for building phylogeny Topology 6

Https://sites.google.com/view/acphyl2017/ Events 1

RelTime rates collapses to a strict clock Software 2

Invariants vs ML (as per Casanellas-Rius and Felsenstein) Topology 4

Workshop Announcement: Taming the BEAST 2017, London, July 2017 Events 1

Unit tests for phylogenetic likelihood computation? Software 10

Phylobayes: alpha, statalpha, rrmean, rrent, statent and Nmode parameters Software 1

Long Branches Attract problem, and forcing a fix on it? Topology 6

Constrained neighbour joining Topology 2

A sane parsimony implementation Software 6

Conferences on Computational Phylogeny in 2017? Events 9

Extended registration deadline to MCEB 2017 Events 1

Videos from 17w5104: Mathematical Approaches to Evolutionary Trees and Networks | Banff International Research Station Events 1

Algebraic and combinatorial phylogenetics (3 weeks in Barcelona) June/July 2017 Events 1

Paper: An experimental phylogeny to benchmark ancestral sequence reconstruction Sequences 1

Cancer Evolution: Postdoc position in Cambridge, UK Positions 1

Is there a NCM simulator? Uncategorized 4

Calculating likelihood of a given tree under birth/death Topology 4

Reconstructing identity of amino acids that are ‘missing data’ in extant sequences Sequences 2

PLL (Phylogenetic Likelihood Library from Stamatakis group) is up Software 10

2017 Workshop on Phylogenomics, Cesky Krumlov, Czech Republic Events 1

Mike Steel’s 2016 predictions Uncategorized 1

Postdoc position in statistical phylogenetics/data analysis Positions 1

Evolutionary Genomics Postdoc in Budapest Positions 1

Ggtree for viewing and annotating phylogenetic tree Software 2

[paper] ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data phyloinformatics 1

[Paper] Site-specific rates of evolution, gamma distribution etc Sequences 3

Manually editing alignments on a mac Software 14

Postdoctoral position in computational epidemiology, Simon Fraser University Positions 1

Ph.D. scholarship on niche modelling with David Bryant, NZ Positions 1

Next Generation Phylogenetic Inference Spotlight Session schedule and abstracts Uncategorized 1

‘T151: New Approaches to Phylogenetic Paleobiology’ at GSA Annual Meeting 2016. Sept 25-28 in Denver Events 2

How to recognize a rearranged tree? Topology 13

[Paper] PUmPER: phylogenies updated perpetually Software 2

Time estimates with rho Dates 1

Testing for ‘sampled ancestors’/sequences at internal nodes Topology 3

Call for papers: RECOMB-Comparative Genomics Events 1

Mike Steel’s 2011 predictions– how is he doing so far? Uncategorized 20

Postdoc position “Evolutionary biology of cancer” in Cambridge UK Positions 1

Mesquite and TreeBASE NEXUS file formats Software 5

File format for defining a taxnomony and clades on a tree Taxa 3

A new view of the tree of life (highlighting the Candidate Phyla Radiation) Taxa 1

Nice review: the shape of phylogenetic tree space Topology 1

Standardized Test Sets for evaluating Software/Methods Sequences 14

Concatenate many genes together for each taxon Software 1

How to handle duplicate sequences efficiently in a phylo-demographic analysis? Dates 3

Genesis SW for post-processing phylogenetic placements Software 5

Email server updates Meta 1

Counting topologies with complex constraints Topology 9

Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations Software 2

Evolution 2016 spotlight session on next-generation phylogenetic inference Events 5

Reconstructing Phylogenetic Tree / missing data Topology 1

What topic would people like to see for the next phyloseminar series? Uncategorized 4

Every new topic will now be posted to the @phylobabble Twitter feed Meta 1

Tree-based measure of species longevity? Dates 6

TreeBase legacy IDs Troubleshooting 6

Summer school announcement: Taming the BEAST, Switzerland, June 2016 Events 1

Phylogenetic Placement Visualization Software 1

Maximum Likelihood tree reconstruction pipeline Topology 5

Maximum parsimony. Wheather the best tree should be completely resolved under this criteria? Topology 2

Troubleshooting RPANDA code Troubleshooting 2

The State of Software in Evolutionary Biology Software 4

Weights used in opposite ways; alignments vs. phylogenetic inference Uncategorized 5

`rotl`, an R package to access the Open Tree of Life data Software 1

2 PhD positions in Stamatakis lab Positions 1

Visualising big trees (again) Software 5

[sprspace] Queries on RMSD and PSRF Troubleshooting 10

Tree comparison using Laplacian spectra Topology 3

Call for Workshop Proposals Events 1

Postdoc in phylogenetics of the immune system Positions 2

[Query] Explain rate matrix in Phylogenetic analysis Troubleshooting 3

p4 Python phylogenetics toolkit Software 1

Compute 2D representation of sequence space without comparing sequences Uncategorized 4

DendroPy 4.0.0 has been released Software 3

Interesting phylogenetic search heuristics Software 4

The interface between Mathematics/Statistics and Phylogenetics – Topics for a talk Uncategorized 6

Two phylo-meetings ‘down-under’ Events 1

Calculating distances with ambiguity codes (R, Y, N etc) in the data Sequences 4

Sustaining a phyloinformatics community post-NESCent Uncategorized 6

Environmental ‘Omics Synthesis Conference 2015 Events 2

Position at Imperial College London to incorporate new phylodynamic models into BEAST Positions 1

Model testing large multigene families Uncategorized 2

Best format(s) for alignments with metadata Practicalities 4

Carbon footprints of phylogenetic analyses? Practicalities 8

Dryad and GPL software Software 5

File Format Converters Practicalities 5

Futurephy website and meetings Events 5

Not so fast, FastTree Software 3

Fitch algorithm for non-binary trees Topology 2

Is it possible to normalize the number of observed SNPs to the size of the genome a good quality call can be made Practicalities 1

DIVERGE - negative thetaML values Troubleshooting 2

Virus Epidemiology and Molecular Evolution Workshop Aug 9 - 14, 2015 Events 1

Concept taxonomy Taxa 8

Complex substitution models and large datasets – how to make it possible to do the analysis Sequences 15

[Paper] Correcting for sequencing error in maximum likelihood phylogeny inference Sequences 4

Mathematical and Computational Evolutionary Biology 2015 Events 1

Geophylogenies using GeoJSON Software 6

[Paper] Phycas: Software for Bayesian Phylogenetic Analysis Software 4

Where to publish a teaching paper Software 3

Mahan Postdoctoral Fellowship at Fred Hutch Positions 1

Tree File Formats. FigTree fails to read TREEBASE Nexus trees? Troubleshooting 2

Supertree workshop Events 1

GBIF Ebbe Nielsen Challenge Events 1

OAuth2 is here; some growing pains Uncategorized 1

iPython Notebook for Phylogenetics Software 12

Free meeting - Sequencing and phylogeny, St Andrews, 8 December Events 1

On age and species richness of higher taxa Dates 7

Next phyloseminar series will be about ARGs; what should we have after that? Events 1

[Paper] Towards more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees Uncategorized 1

Sampling from the SPR random walk on rooted trees Topology 10

Pruning an alignment, rows or columns Practicalities 5

[Paper] The space of ultrametric phylogenetic trees Topology 1

PhyloType web server Software 1

Fast log likelihood given a fixed alignment, fixed tree, and fixed huge arbitrary sparse transition rate matrix Uncategorized 3

A good dataset for undergraduate coursework Troubleshooting 7

[Paper] Hypermutable DNA chronicles the evolution of human colon cancer Sequences 7

Predicting evolution from the shape of genealogical trees Uncategorized 1

How to measure the phylogenetic signal, vs random noise in a data set? Homology 1

Prunning off long branches Practicalities 3

Conversion of BEAST XML alignments to PHYLIP format Practicalities 2

Feedback please! Meta 12

Phylogenetic placement of marker gene amplicons as operational taxonomic units Taxa 7

Correlation between multistate characters Uncategorized 3

Visualizing conflicting trees with different sampling? Practicalities 6

LaTeX and code blocks Meta 2

What to do if AU test accepts a hypothesis, while SH test rejects with a p-value of 0 Topology 2

How to get Accession numbers by sequences or “gi numbers” in Genbank in a batch-job manner? Troubleshooting 6

[Paper] Timing and order of transmission events is not directly reflected in a pathogen phylogeny Dates 1

Problems with recent Drosophila phylogeny Uncategorized 3

[Paper] Efficient Continuous-Time Markov Chain Estimation (in very large state spaces) Sequences 1

Number of bootstrap replicates for short alignments Topology 8

ETE-NPR: Nested Phylogenetic Reconstruction and workflow design Software 1

[Paper] Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection Uncategorized 3

Viewing a Lagrange tree Practicalities 7

Phylobayes: how to measure the compositional heterogeneity of each taxa Software 1

Eddie Homes on “The Greatest Experiment in Evolution: Viral Biocontrol of Rabbits” April 15 (in Scotland) Events 3

[Paper] The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates Dates 3

Postdoc: insect systematics and biodiversity informatics Positions 1

Phylobayes: maxdiff calculation on more than 2 chains Software 5

Reading codon alphabets, when you have ambiguity codes Software 10

Quantifying support in the face of missing data Sequences 11

`ape` gods: how should I go about doing phylogenetic diversity calculations on a tree? Traits 10

Paper developing a new approach to phylogenetic tree shape Topology 5

Feedback on new web-based very large tree viewer Software 22

About parsing newick format Taxa 1

Inline phylogeny from Newick description Meta 3

19th annual New Zealand phylogenomics conference (Feb. 2015) Events 1

Additive distance matrices, caterpillar trees, and validation of cluster analysis Troubleshooting 3

Mathematical Phylogeny from Mike Steel June 28 - July 2, 2014 in South Carolina Events 1

Description of the MrBayes parsimony-based proposals Topology 2

The SNAD Sequence Renaming tool Practicalities 2

[Paper] Phylotastic A NESCent project Software 1

[Paper] Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes Dates 2

Postdoc: help design next HIV vaccine trials using molecular evolution Positions 1

[Paper] Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads Software 1

Current best practice for simulating viral sequences? Sequences 12

How to improve external node support on a supertree? Topology 1

We have an RSS feed now Meta 3

DIstance-based methods and incomplete sequence matrix Sequences 4

How to infer topology and clade support with very low diversity alignments? Topology 24

Graphing identical sequences on phylogenetic tree using R and APE Practicalities 3

PhD thesis unknown to me, which does Bayesian inference of a tree of cells, as well as many other things Uncategorized 2

Bayesian Phylogenetics Workshop Events 1

Best mechanism to report negative results Uncategorized 5

Oneboxes for PubMed Meta 8

Phyloinformatics GSOC application post-mortem? Software 3

Matrix Data types Troubleshooting 6

Matrix strategies to avoid rate matrix exponentiation Sequences 4

[Paper] Phylogenetic Stochastic Mapping without Matrix Exponentiation Traits 38

Let’s quantify the impact of missing data Sequences 19

B cell receptor within-host molecular evolution Sequences 2

DNA or protein sequence identity vs true phylogenetic distance Homology 1

Genomic Classification: A(nother) novel attempt Taxa 3

What sorts of categories should we have? Meta 28

Building a tree for all DNA barcodes (> 1 million taxa) Uncategorized 6

Extending NEXUS TREE block Software 10

Species delimitation in BEAST Software 1

Upcoming talk on phylogenetic MCMC mixing using SPR distance Topology 9

Can one hear the shape of a population history? Dates 2

Statistical consistency of OTOL methods? Topology 3

ExaBayes: Bayesian phylogenetic reconstruction of large data sets Software 5

[Paper] A synchronized global sweep of the internal genes of modern avian influenza virus Dates 11

[Paper] An experimentally determined evolutionary model dramatically improves phylogenetic fit Sequences 3

21st International HIV Dynamics & Evolution conference, May 7-10 Events 1

[Paper] Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2 Traits 1

Schedule and video for “Computation-Intensive Probabilistic and Statistical Methods for Large-Scale Population Genomics” Feb 18-21 Events 2

Discourse settings discussion Meta 7

Discourse Admin Quick Start Guide Uncategorized 2