attach full raxml-ng log, then I will see what is going on. Best, Oleksiy On 14.05.25 15:12, Rachel Isaac wrote: > I am running an alignment of about 6000 sequences with a length of

> Although RAxML-NG is generally faster, v1.x does not implement rapid > bootstrapping, which means that > for your analysis it could even be slower. > > However, you

for both raxml-ng and IQ-TREE. Please note that I kept receiving a numerical underflow warning with IQ-TREE. I brought this up on their discussion board and was told that the results

re feeding RAxML with data > that struggles to inform a tree. Eg a dataset with a lot of > near-identical tips or a multigene sample with a lot of reticulate signal > imbedded

in the raxml google group to try and > find advice for dealing with > > my particular dataset (many taxa, short alignment). > > > > In your previous reply you stated

searches for RAxML-NG or vice versa for RAxML8. Thus I made all-in-one analyses using RAxML8 and the original and fast versions of RAxML-NG for the same eight data sets. The results

is somewhat slower, but on the dataset like yours the difference will be negligible. I will keep you posted. Best, Alexey On 21.04.22 15:16, Alexey Kozlov wrote: > Hello, > >

smooth at RAXML and this > is the current status (attached screenshot). I was running rapid 100 > bootstraps and 20 ML trees to get the best tree. > > 1)What remaining steps

version of raxml-ng. thanks for reporting! > Anyway, I didn't know it would make raxml-ng slower. I thought raxml-ng would use reduced phy file > and reduced newick file

amkozlov/raxml-ng/releases/tag/1.0.1 Best, Alexey On 22.10.20 18:26, Sara Rocha wrote: > Hi, > related question, is there a way in RaxML-NG to have the boots written to a file

reran with RAxML v8 using GTRGAMMAX. RAxML-ng still wins (ML > -1068519.089387 for the new > > run). Any idea why RAxML-ng is 3x slower? > > Because raxml-ng search heuristic

in your raxml-ng command as you have specified in your resource requests? I did this by accident and the jobs did run but the calculations were about 20 times slower (than when --cpus

of steps RAxML-NG will > perform or it is data-dependent? I mean, 4 rounds of AUTODETECT spr, then 4 rounds of FAST spr, then The order of steps is fixed, but the number of iterations

partitions.raxml.partitions -o > Sphenodon_punctatus-g gekko.tre -T 10-p 12345-n gekkoTest > | > > Correct output file attached. > > > > > On Thursday

my other raxml-pthreads run >>>> finished... >>>> >>>> cheers, >>>> andrea >>>> >>>> On Tuesday

30% slower, but should be more reliable. Best, Alexey 2018-08-13 18:34 GMT+02:00 : > Hi Alexey, > > Thanks! I tried ModelTest-NG, but there was an error with the latest >

hopefully rerunning RAxML. > > Appreciate all of the help, > > Camille > > On Tuesday, June 26, 2018 at 12:37:38 PM UTC-5, Alexey Kozlov wrote: > > Hi Camille

parallelism at RAxML? yes we do If so, I may be better sticking with RAxML for the time being as MPI+Pthreads > appeared to work ok. I am curious though why running a hybrid MPI/Pthreads

general, RAxML-NG could be slower than RAxML for some specific datasets and settings, although those are really rare individual cases. I observed it just a couple of times among dozens

, whereas RAxML-NG uses the random ones. so in order to make both analyses equivalent you'd need to add "-d" option to the raxmlHPC-AVX command line On 26.10.2017 17

command in RAxML-NG? > > Better said, do I need to control these seeds or every individual > instance will automatically get a random seed? > > That's true, each

by using NG for final GAMMA optimization. >I only ask because NG is about an order of magnitude slower on my system than ExaML, and the difference widens further >if I use '