Groups
Conversations
All groups and messages
Send feedback to Google
Help
Training
Sign in
Groups
slim-discuss
Conversations
About
slim-discuss
Contact owners and managers
1–30 of 634
Welcome to
slim-discuss
! Please find general information and downloads for SLiM at
http://messerlab.org/slim/
. There is a free online SLiM workshop at
http://benhaller.com/worksh
ops/workshops.html
.
IF YOU WISH TO JOIN, YOU MUST SUPPLY A SLIM-RELATED "REASON FOR JOINING" IN YOUR REQUEST.
This is how we keep spammers out of the group.
Mark all as read
Report group
0 selected
Jared Grummer
, …
Ben Haller
13
Mar 26
Linked variable and diagnostic SNPs
Hi Ben, Thank you. I have that section highlighted and I've just re-read through it a couple
unread,
Linked variable and diagnostic SNPs
Hi Ben, Thank you. I have that section highlighted and I've just re-read through it a couple
Mar 26
yang lu
,
Ben Haller
3
Mar 26
Over specific mutation frequency under admixture model
Hi! Your previous email to the list doesn't seem to have gotten posted correctly for some reason,
unread,
Over specific mutation frequency under admixture model
Hi! Your previous email to the list doesn't seem to have gotten posted correctly for some reason,
Mar 26
Lou GUYOT
,
Ben Haller
2
Mar 26
Follow recombinant individuals
Hi Lou! I'd recommend that you read about tree-sequence recording in the manual; using that, you
unread,
Follow recombinant individuals
Hi Lou! I'd recommend that you read about tree-sequence recording in the manual; using that, you
Mar 26
Soumitra Bhide
,
Ben Haller
2
Mar 25
mutationEffect query
Hi Soumitra! No, they are not the same. If you have just a single m4 mutation in your model, they
unread,
mutationEffect query
Hi Soumitra! No, they are not the same. If you have just a single m4 mutation in your model, they
Mar 25
Ben Haller
Mar 22
SLiM 4.2 released
Hi folks! SLiM 4.2 has just been released. This is a major point release with some new features that
unread,
SLiM 4.2 released
Hi folks! SLiM 4.2 has just been released. This is a major point release with some new features that
Mar 22
Daiki Tagami
,
Ben Haller
3
Mar 21
Modeling effect size
Hi Ben, Thank you very much for your reply. I also had a conversation with Peter about it, and he
unread,
Modeling effect size
Hi Ben, Thank you very much for your reply. I also had a conversation with Peter about it, and he
Mar 21
yang lu
,
Ben Haller
2
Mar 16
Ancestral tracts
Hi! I think gene conversion tracts are recorded as part of tree-sequence recording, yes. You might be
unread,
Ancestral tracts
Hi! I think gene conversion tracts are recorded as part of tree-sequence recording, yes. You might be
Mar 16
Ivan Scotti
,
Ben Haller
5
Mar 16
Inconsistent MacOs GUI vs Linux command line script behaviour?
Hi Ivan! I'm not a conda user, so I don't know. My guess would be that you had both 3.7.1 and
unread,
Inconsistent MacOs GUI vs Linux command line script behaviour?
Hi Ivan! I'm not a conda user, so I don't know. My guess would be that you had both 3.7.1 and
Mar 16
Tiina Sävilammi
, …
Ben Haller
6
Mar 14
Neutral evolution with custom reference fasta and SNPs
Hi Tiina! Yes, combine the individuals into one VCF, and read that VCF into a nonWF model (it has to
unread,
Neutral evolution with custom reference fasta and SNPs
Hi Tiina! Yes, combine the individuals into one VCF, and read that VCF into a nonWF model (it has to
Mar 14
Ben Haller
2
Mar 13
SLiM today TODAY!
The video of this talk has been posted on the SLiM home page, which now has a "Videos"
unread,
SLiM today TODAY!
The video of this talk has been posted on the SLiM home page, which now has a "Videos"
Mar 13
Aude Caizergues
, …
Peter Ralph
5
Mar 12
Reaching equilibrium with recapitation
Hello, My apologies for the late update. You were right about your guess, I indeed completely missed
unread,
Reaching equilibrium with recapitation
Hello, My apologies for the late update. You were right about your guess, I indeed completely missed
Mar 12
Prothama Manna
,
Ben Haller
2
Mar 7
calcHeterozygosity in every 10 generation
Hi Prothama, The createLogFile() call has a logInterval parameter. You are currently passing 1 for
unread,
calcHeterozygosity in every 10 generation
Hi Prothama, The createLogFile() call has a logInterval parameter. You are currently passing 1 for
Mar 7
Anil Ori
,
Ben Haller
5
Mar 6
calculating pairwise LD in simulation
Hi Anil, OK, since you only need to calculate LD for your post-run analysis, and since you need it
unread,
calculating pairwise LD in simulation
Hi Anil, OK, since you only need to calculate LD for your post-run analysis, and since you need it
Mar 6
Mariadaria Ianni-Ravn
, …
Ben Haller
5
Feb 27
Average lifetime of mutations?
Hi all! For me, outputting the sim.mutation.ids at every generation worked very well - the solution
unread,
Average lifetime of mutations?
Hi all! For me, outputting the sim.mutation.ids at every generation worked very well - the solution
Feb 27
Hannes Becher
,
Ben Haller
3
Feb 23
delimited output?
Hi Hannes! Yes, your solution is fine. It can be useful that Eidos allows both single and double
unread,
delimited output?
Hi Hannes! Yes, your solution is fine. It can be useful that Eidos allows both single and double
Feb 23
meagha...@gmail.com
,
Peter Ralph
3
Feb 22
Unique individuals with same nodes?
Hi Peter, Thanks so much for your prompt reply! Thinking about nodes in terms of the node table
unread,
Unique individuals with same nodes?
Hi Peter, Thanks so much for your prompt reply! Thinking about nodes in terms of the node table
Feb 22
Jaskaran Singh Gill
,
Ben Haller
4
Feb 18
how to reset tick
Hi Jaskaran, I think I already answered your question...? Please see the manual section I recommended
unread,
how to reset tick
Hi Jaskaran, I think I already answered your question...? Please see the manual section I recommended
Feb 18
wpearm...@gmail.com
, …
bob
4
Feb 14
Modelling microbiomes/many species communities
Hi Ben & Bob, Thank you both for replying! Rather than aiming for 'full-size' populations
unread,
Modelling microbiomes/many species communities
Hi Ben & Bob, Thank you both for replying! Rather than aiming for 'full-size' populations
Feb 14
Perry Xu
, …
hyan...@googlemail.com
8
Feb 7
position column in the vcf file produced by tskit write_vcf not correct
Hi Perry I should also add that the REF value output by the tskit write_vcf() function is always
unread,
position column in the vcf file produced by tskit write_vcf not correct
Hi Perry I should also add that the REF value output by the tskit write_vcf() function is always
Feb 7
Luis Fernández
,
Ben Haller
2
Feb 5
Getting repeat counts instead of snp calls in the vcf
Hi! I assume you're seen section 14.11 of the manual, on modeling microsatellites. :-> I'd
unread,
Getting repeat counts instead of snp calls in the vcf
Hi! I assume you're seen section 14.11 of the manual, on modeling microsatellites. :-> I'd
Feb 5
Svitlana Braichenko
,
Ben Haller
11
Feb 2
Balancing selection with preferred frequency in nucleotide models
Great! :-> A note for posterity: I should have written "With a dominance coefficient of 1.5
unread,
Balancing selection with preferred frequency in nucleotide models
Great! :-> A note for posterity: I should have written "With a dominance coefficient of 1.5
Feb 2
Devashish Tripathi
,
Ben Haller
3
Feb 2
Sex ratio becomes zero after loading msprime sequence in SLiM
I'm glad you found the problem, Devashish, because I was a bit mystified! Sounds like there might
unread,
Sex ratio becomes zero after loading msprime sequence in SLiM
I'm glad you found the problem, Devashish, because I was a bit mystified! Sounds like there might
Feb 2
Devashish Tripathi
,
Ben Haller
2
Feb 1
Setting up 2D stepping stone model with manual allocation of population
Hi Devashish! Your model looks like it is working fine to me. The subpopulations print in sorted
unread,
Setting up 2D stepping stone model with manual allocation of population
Hi Devashish! Your model looks like it is working fine to me. The subpopulations print in sorted
Feb 1
Iago-lito -
Feb 1
Refresh eidos file when edited from another program.
Hello, I am currently working my way through the online workshops. Thank you for this sweet piece of
unread,
Refresh eidos file when edited from another program.
Hello, I am currently working my way through the online workshops. Thank you for this sweet piece of
Feb 1
Gabriele Sgarlata
,
Ben Haller
4
Jan 31
A discrete QTL effects model with nucleotide-based mutations and initial standing variation
Hi Gabriele, Regarding "I had used a realistic mutation rate (1e-8) and still over tens/hundreds
unread,
A discrete QTL effects model with nucleotide-based mutations and initial standing variation
Hi Gabriele, Regarding "I had used a realistic mutation rate (1e-8) and still over tens/hundreds
Jan 31
michelle Kim
,
Ben Haller
2
Jan 31
Sample output
Hi Michelle! So, the first place to go to answer your question might be the reference documentation
unread,
Sample output
Hi Michelle! So, the first place to go to answer your question might be the reference documentation
Jan 31
Gregor Gorjanc
, …
Peter Ralph
4
Jan 30
How long do large simulations take?
Ben & Peter thanks! We will run pilot scaling runs and see how far we will get. Will try to
unread,
How long do large simulations take?
Ben & Peter thanks! We will run pilot scaling runs and see how far we will get. Will try to
Jan 30
Max Shpak
,
Ben Haller
2
Jan 29
number of mutations introduced with addNewDrawnMutation
Hi Max, For the script you quoted, there are no "both chromosomes of target". The target
unread,
number of mutations introduced with addNewDrawnMutation
Hi Max, For the script you quoted, there are no "both chromosomes of target". The target
Jan 29
Annabel Perry
,
Ben Haller
3
Jan 19
Treating Mutations with Different Populations-of-Origin as the Same SNP
Thank you! I'll give these sections a read and try to solve this On Friday, January 19, 2024 at
unread,
Treating Mutations with Different Populations-of-Origin as the Same SNP
Thank you! I'll give these sections a read and try to solve this On Friday, January 19, 2024 at
Jan 19
Dylan Clark
,
Ben Haller
5
Jan 18
initialize recombination rate vs addrecombinant
Awesome thank you! On Thursday, January 18, 2024 at 12:11:13 PM UTC-8 Ben Haller wrote: Hi Dylan, You
unread,
initialize recombination rate vs addrecombinant
Awesome thank you! On Thursday, January 18, 2024 at 12:11:13 PM UTC-8 Ben Haller wrote: Hi Dylan, You
Jan 18