lutteropp/NetRAX

Issues

• Run-time error: help needed

  #87 opened 2 years ago by yufengwudcs
  3

• Trouble with options --max_reticulations and --brlen

  #86 opened 2 years ago by max-hill
  2

• Comparison with PhyLiNC, PhyloDAG, SNAQ, PhyloNET MPL, and PhyloNET ML on simulated data

  #83 opened 3 years ago by lutteropp
  34

• Detailed Future Work Ideas

  #85 opened 3 years ago by lutteropp
  1

• Snakes Empirical Dataset

  #82 opened 3 years ago by lutteropp
  18

• Noncritical bug in deciding how often to repeat nontopology optimization

  #84 opened 3 years ago by lutteropp
  0

• Simulated experiments for paper, result files

  #81 opened 3 years ago by lutteropp
  9

• Empirical dataset

  #48 opened 4 years ago by lutteropp
  5

• New experimental setup

  #46 opened 4 years ago by lutteropp
  28

• Idea for a fast, CLV-based network pseudolikelihood

  #60 opened 4 years ago by lutteropp
  5

• Speed up ranking of candidates

  #53 opened 4 years ago by lutteropp
  2

• Less stupidly adding reticulations

  #50 opened 4 years ago by lutteropp
  3

• Derivative of Network Loglikelihood for brlen optimization

  #49 opened 4 years ago by lutteropp
  44

• [for later, just curious] Question about Branch Length Optimization

  #43 opened 4 years ago by lutteropp
  48

• A short observation about per-displayed-tree-clvs

  #47 opened 4 years ago by lutteropp
  10

• I don't understand those Dendroscope network distances

  #13 opened 4 years ago by lutteropp
  13

• Unrooted softwired distance

  #45 opened 4 years ago by lutteropp
  9

• [for later, just curious] Question about Ancestral State Reconstruction

  #41 opened 4 years ago by lutteropp
  10

• New experimental results

  #42 opened 4 years ago by lutteropp
  19

• Evaluation of true network weirdness not working

  #44 opened 4 years ago by lutteropp
  2

• NetRAX needs a Log File

  #16 opened 4 years ago by lutteropp
  1

• Rewrite and Extend the Plot Script

  #29 opened 4 years ago by lutteropp
  0

• Can the current horizontal moves fix a badly placed reticulation?

  #34 opened 4 years ago by lutteropp
  8

• Observation: The number of reticulations depends on the chosen brlen linkage mode (and maybe also on the likelihood model)

  #33 opened 4 years ago by lutteropp
  7

• Should we exclude datasets where the simulated network has worse BIC than the raxml-ng best tree?

  #40 opened 4 years ago by lutteropp
  3

• Change to Network Search Algorithm to get rid of 0/1 reticulation probs in final result

  #36 opened 4 years ago by lutteropp
  6

• NetRAX needs to return not only the best inferred network (in terms of BIC), but also best inferred network for 1 more reticulation

  #39 opened 4 years ago by lutteropp
  4

• BUG: Something is odd in hillClimbingStep

  #26 opened 4 years ago by lutteropp
  4

• When and in which order optimize reticulation probs, branch lengths, and model parameters?

  #37 opened 4 years ago by lutteropp
  2

• Switch to Search in Waves

  #30 opened 4 years ago by lutteropp
  9

• Bug with Arc Removal Move

  #38 opened 4 years ago by lutteropp
  2

• Is this a bug or not? (Non-deterministic result for 1-reticulation network, sometimes bad reticulation probabilities)

  #32 opened 4 years ago by lutteropp
  25

• Effect of branch-length linkage on Network inference

  #28 opened 4 years ago by lutteropp
  2

• Implement Network Checkpointing

  #35 opened 4 years ago by lutteropp
  0

• Parallelize NetRAX

  #31 opened 4 years ago by lutteropp
  1

• Do not re-simulate the MSA when switching only the LikelihoodType in experiments

  #24 opened 4 years ago by lutteropp
  4

• Verification of the BIC Computation

  #22 opened 4 years ago by lutteropp
  19

• BUG: NEPAL-like re-estimation of reticulation probabilities leads to worse BIC score when more than 1 partitions are present

  #25 opened 4 years ago by lutteropp
  13

• Network Inference in Unpartitioned Datasets

  #27 opened 4 years ago by lutteropp
  1

• BUG: NetRAX treats partitioned MSA as non-partitioned (wrong command line call?)

  #23 opened 4 years ago by lutteropp
  16

• Verification of the partitioned MSA generated by using SeqGen

  #21 opened 4 years ago by lutteropp
  4

• Discussion of Experimental Results for "small_network" (4-10 taxa, 1-2 reticulations)

  #19 opened 4 years ago by lutteropp
  18

• Does LikelihoodType.BEST make any sense at all, if we use BIC to score networks?

  #20 opened 4 years ago by lutteropp
  13

• Experimental Results for running NetRAX on tiny datasets (4-10 taxa) are here!

  #17 opened 4 years ago by lutteropp
  12

• Discussion of Experimental Results for "small_tree" (4-10 taxa, 0 reticulations)

  #18 opened 4 years ago by lutteropp
  4

• Profiling a NetRAX run on a tree dataset

  #12 opened 4 years ago by lutteropp
  15

• Experiment Plot planning for Tree Simulations

  #15 opened 4 years ago by lutteropp
  11

• Explanation of the current Experimental Results CSV Header

  #14 opened 4 years ago by lutteropp
  8

• 100 simulated MSA sites on 10-taxon-tree is not enough for RAxML

  #11 opened 4 years ago by lutteropp
  6

• How to score an input network? With or without changing branch lengths?

  #10 opened 4 years ago by lutteropp
  2