sfscode-updates — Very low traffic mailing list to announce software updates (recommended).

[sfscode-updates] SFS_CODE Update: 2015-08-15

[Ryan H. <rh...@gm...>]

Dear SFS_CODE'ers,

I've posted an update to SFS_CODE to the project page.  There are several
updates, including bug fixes and new features.  You can read about them in
the Release Notes pasted below.

Let me know if you have any questions.

Happy simulating!

Ryan

****  CURRENT RELEASE:  ****


DATE:  2015-08-15


NEW FEATURES:

    Generally much faster.  I made a few improvements to the way data
structures are handled.


    optimizeLL.pl

        When simulating long loci, SFS_CODE can be slow.  This is because
it stores only unique haplotypes, and there can be many unique haplotypes
with a long locus.  By dividing the locus into chunks, you gain the ability
to store far few haplotypes.  Optimizing this used to be a fairly arbitrary
process.  I've created a heuristic solution to this problem called
optimizeLL.pl. It will run a very simple version of your desired
constraints (population size, locus length, etc), and find the optimal
partitioning of the loci to minimize runtime.


    --VCF

        now output directly to VCF files.


    --selDistType (-W) ... [H <h>] ...

        This option now allows dominance! Note that h=1.0 is codominance
for backwards compatibility. Arbitrary models of dominance are allowed,
using the same distributions as the selection coefficients (1: constant, 2:
gamma distribution, 3: normal distribution).


    --mutation ... [H <h>] ... [F <file>]

        This option now allows dominance [H] as above, and the ability to
simulate a conditional trajectory.  The idea is that you can generate a
trajectory using another software (or outputing the trajectory from an
SFS_CODE simulation), and input it here to fix the path of a given mutation
and simulate linked loci under the resulting structured population.


BUG FIXES:

    --indel and --longIndel no longer delete more sequence than is
possible.  Previously, it was possible to have a 10bp deletion that occured
at the last position of the simulated sequence, effectively deleting DNA
from the end of the chromosome.  Thanks to William Nicholson for pointing
this out.


    The way --neutPop worked did not maintain neutrality in the indicated
populations in some situations.  This has been fixed.


    Many fixes in convertSFS_CODE, which had caused may people problems...
My apologies for taking so long!

[sfscode-updates] SFS_CODE updates!

[Ryan H. <rh...@gm...>]

Hi Folks,

It has been a while, but I've made some significant updates to SFS_CODE!
 You can find a description in the release notes below.  This release
includes some new features, and importantly, some significant optimizations
to the code.  It is now tremendously faster than it was, and returns
SFS_CODE to being one of the fastest forward simulation programs out there!

Best,

Ryan


DATE:  2014-07-19

This release includes two primary bug fixes, a couple of additional
features, and a major efficiency optimization.

BUGS:

Bug 1:  Time to fixation conditional on fixation.  This should affect only
simulations where a large number of bases are simulated (e.g., 1Mb or
larger), and you are looking at the time to fixation conditional on
fixation for mutations in a small simulated chunk (e.g., 1kb).  This could
arise when you are interested in a locus surrounded by deleterious
background, or if you are simulating an exome.  The previous version
reported fixation times that were too large.  This did not impact
segregating variants.

Bug 2:  Recombination.  Previously, when the number of recombination events
were low (e.g., when the simulated number of recombination events entering
a population in a given generation was < 0.1*N for the population), the
recombination events were only being distributed amongst females (though
both maternal and paternal chromosomes were recombining, only females
inherited recombinant chromosomes).  This has been resolved.

NEW FEATURES:

Output Samples:  You can now output samples throughout the simulation.
 This is implemented as an extension of the -n flag to a -Tn timed event.
 Note that -n still works as before, but if you use -Tn, you can now
indicate specific times to sample the population, or specify a regular
interval to sample the population.  The -Tn option changes the output
slightly, adding a flag like "//gen=XX" prior to the sequence data at that
time point.  The final sample is still taken and reported as usual.  Here
is the updated description:

-n*  --sampSize  [P <pop>] [R <tau_d>] [S <tau_1>]] <SS1>
[<SS2>...<SSNpops>]
     set the number of individuals sampled from a population.  When used
     as -Tn, a time must be specified for sampling, and opens the ability
for
     [R]ecurrent sampling starting at the pre-specified time, and repeat
every
     tau_d*PN_A generations until the end of the simulation, or a specified
     [S]top time tau_1.  Note that the sample size must be specified at the
     end (either a single number to be applied to all populations or include
     a number for every population).  You can use -Tn multiple times.


Soft Sweeps:  You can now do a form of selection on standing variation in
SFS_CODE.  This is implemented through the -TW argument.  You need to
specify the time that selection starts, the allele frequency, and the type
of selection you want to act on it.  SFS_CODE will find a random allele
that ideally is at the specified frequency F +/-0.05F. If a SNP cannot be
found in this range, the SNP nearest in frequency will be used.  Here is
the updated description:

-W*  --selDistType  [P <pop>] [L <locus>] [F <allele_freq> [w] [T [R
<min_freq> <max_freq> [S]] [A [G <gens>]] [M <max_reps>] [F [a] <file>]]]
<type> [args]
     set distribution of selective effects.  See documentation for proper
     usage of <type> [args].  Set the distribution for a [P]opulation or
     [L]ocus.  In -TW mode, change selection coefficient of an existing
     polymorphism with a particular [F]requency.  If a frequency is
specified,
     you can [T]rack the allele to ensure that it achieves a particular
     frequency [R]ange at time of sampling ([S]topping the first time in
range),
     [A]utomatically restart if the allele is lost (up to a [M]aximal
number of
     tries), and output the trajectory to a [F]ile (or [a]ppend to
existing).
     Note that tracking a mutation here prevents you from tracking a locus
using
     --trackTrajectory.  Unfortunately, tracking only occurs after selection
     coefficient changes.


OPTIMIZATIONS:

For simulations with long sequences and/or large numbers of individuals,
SFS_CODE was rather slow.  This is partly because there were a few
redundant calculations being performed on each mutation every generation.
 As generations went on and the number of variants (both fixed and
polymorphic) grew, this led to a roughly exponential growth in computation
time per generation.  Eliminating these redundant calculations has resulted
in a DRAMATIC increase in efficiency for long sequences and/or large
numbers of individuals.

[sfscode-updates] SFS_CODE update

[Ryan H. <rhe...@uc...>]

Hello SFS_CODEers,

Several new features (some long awaited) to announce!!

1)  --admixture (-TJ)
You can now directly simulate admixture!  The options are extremely
flexible, allowing for an arbitrary number of ancestral populations,
differing representation of males and females from ancestral populations,
etc.

2)  --mutation
Introduce a new mutation at any time, with a user-specified selection
coefficient!
3)  --trackAncestry
This allows you to know the true genetic ancestry of individuals at every
site when you are simulating with migration or admixture.  Very handy to
know the exact widths and locations of each admixture block.
4)  --trackTrajectory
Follow the frequency trajectory of a mutation generation by generation.
 This option can also be used to specify the final frequency of a derived
allele at the time of sampling, and automatically restart the simulation if
all the mutations you are tracking are fixed or lost.

Updates:
I have fixed the way that convertSFS_CODE creates ms-style output so that
the output can be used directly with sample_stats (supplied with the ms
download).


Download the new version, and try out the new features:
http://sfscode.sourceforge.net/

[sfscode-updates] Fwd: [SourceForge.net Release] sfscode : sfscode

[Ryan H. <rh...@gm...>]

A new version of sfs_code has been released!  The major new addition is gene
conversion, which can also allow for biased gene conversion.  I've also
added a few other features such as an additive model of selection, which are
all described in the users manual.

As always, comments are very welcome.

Happy simulating!

-Ryan

---------- Forwarded message ----------
From: SourceForge.net <no...@so...>
Date: Thu, Feb 19, 2009 at 6:19 PM
Subject: [SourceForge.net Release] sfscode : sfscode
To: no...@so...


Project: sfs_code  (sfscode)
Package: sfscode
Date   : 2009-02-19 19:19

Project "sfs_code" ('sfscode') has released the new version of package
'sfscode'.
You can download it from SourceForge.net by following this link:
<
https://sourceforge.net/project/showfiles.php?group_id=211239&release_id=662521
>
or browse Release Notes and ChangeLog by visiting this link:
<https://sourceforge.net/project/shownotes.php?release_id=662521>

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of this package were released. If you don't wish to be notified in the
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-- 
***************************************
Ryan D. Hernandez
Postdoctoral Researcher
Human Genetics
University of Chicago
418 CLSC
Chicago, IL  60637

email: rhe...@uc...
phone:  (773) 834-8932

[sfscode-updates] Fwd: [SourceForge.net Release] sfscode : sfscode

[Ryan H. <rhe...@uc...>]

Through ongoing testing of sfs_code, I discovered a bug when exactly 2 loci
were simulated with partial linkage (no recombination events were thrown
down between the loci).  I've corrected the error, and posted a new version
on the website below.

I will be submitting a manuscript on sfs_code in the next day or two.

Happy Simulating!

-Ryan

---------- Forwarded message ----------
From: SourceForge.net <no...@so...>
Date: Mon, Aug 11, 2008 at 12:14 PM
Subject: [SourceForge.net Release] sfscode : sfscode
To: no...@so...


Project: sfs_code  (sfscode)
Package: sfscode
Date   : 2008-08-11 12:14

Project "sfs_code" ('sfscode') has released the new version of package
'sfscode'.
You can download it from SourceForge.net by following this link:
<
https://sourceforge.net/project/showfiles.php?group_id=211239&release_id=619186
>
or browse Release Notes and ChangeLog by visiting this link:
<https://sourceforge.net/project/shownotes.php?release_id=619186>

You receive this email because you requested to be notified when new
versions
of this package were released. If you don't wish to be notified in the
future,
please login to SourceForge.net and click this link:
<
https://sourceforge.net/project/filemodule_unmonitor.php?filemodule_id=253795
>
If you lost your SourceForge.net login name or password, refer to this
document:
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Note that you may receive this message indirectly via one of your mailing
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mailings.



-- 
***************************************
Ryan D. Hernandez
Postdoctoral Researcher
Human Genetics
University of Chicago
418 CLSC
Chicago, IL 60637

email: rhe...@uc...
phone: (773) 834-8932

[sfscode-updates] Fwd: [SourceForge.net Release] sfscode : sfscode

[Ryan H. <rh...@gm...>]

---------- Forwarded message ----------
From: SourceForge.net <no...@so...>
Date: Tue, Jul 29, 2008 at 5:59 PM
Subject: [SourceForge.net Release] sfscode : sfscode
To: no...@so...


Project: sfs_code  (sfscode)
Package: sfscode
Date   : 2008-07-29 17:59

Project "sfs_code" ('sfscode') has released the new version of package
'sfscode'.
You can download it from SourceForge.net by following this link:
<
https://sourceforge.net/project/showfiles.php?group_id=211239&release_id=616488
>
or browse Release Notes and ChangeLog by visiting this link:
<https://sourceforge.net/project/shownotes.php?release_id=616488>

You receive this email because you requested to be notified when new
versions
of this package were released. If you don't wish to be notified in the
future,
please login to SourceForge.net and click this link:
<
https://sourceforge.net/project/filemodule_unmonitor.php?filemodule_id=253795
>
If you lost your SourceForge.net login name or password, refer to this
document:
<https://sourceforge.net/docman/display_doc.php?docid=760&group_id=1>

Note that you may receive this message indirectly via one of your mailing
list
subscriptions. Please review message headers before reporting unsolicited
mailings.



-- 
***************************************
Ryan D. Hernandez
Postdoctoral Researcher
Human Genetics
University of Chicago
418 CLSC
Chicago, IL 60637

email: rhe...@uc...
phone: (773) 834-8932

Re: [sfscode-updates] Memory leak fixed: 06/29/2008

[Ryan H. <rh...@gm...>]

The previous post did not go through, so I'm trying my gmail account.  Let
me know if you actually receive this email.

Thanks!

Ryan

On Sun, Jun 29, 2008 at 4:03 PM, Ryan Hernandez <rhe...@uc...>
wrote:

> SFS_CODE had a memory leak when performing multiple simulations with
> multiple populations across multiple loci.  This should not have affected
> any previous results, just makes the program a bit more sound.  Thanks
> valgrind!
>
> A new release has been posted on sourceforge:  sfscode.sourceforge.net.
>
> happy simulating!
>
> Ryan
>



-- 
***************************************
Ryan D. Hernandez
Postdoctoral Researcher
Human Genetics
University of Chicago
418 CLSC
Chicago, IL 60637

email: rhe...@uc...
phone: (773) 834-8932

[sfscode-updates] Memory leak fixed: 06/29/2008

[Ryan H. <rhe...@uc...>]

SFS_CODE had a memory leak when performing multiple simulations with
multiple populations across multiple loci.  This should not have affected
any previous results, just makes the program a bit more sound.  Thanks
valgrind!

A new release has been posted on sourceforge:  sfscode.sourceforge.net.

happy simulating!

Ryan

[sfscode-updates] working out the kinks

[Ryan H. <rh...@gm...>]

Hello,

As it turns out, I'm still working out the kinks on putting files together
for upload.  I've you've already downloaded SFS_CODE, please download again
(one of the files was not right, and the documentation left out the
information on simulating indels).  If not, then no worries.

Cheers!

Ryan

http://sfscode.sourceforge.net

[sfscode-updates] SFS_CODE released!

[Ryan H. <rh...@gm...>]

The SFS_CODE source code has finally been released!  It is not quite
"pretty" code, but it has been tested against coalescent simulations in a
wide range of cases and shown to be quite accurate.  I've also compared
site-frequency spectra under various selective effects with and without
demography to their Poisson Random Field expectations.  In each case, the
program performs very well.  The details of these simulation tests will be
posted on the website at http://sfscode.sourceforge.net (or on the
sourceforge wiki if I get adventurous) in the near future.  I'll also
include performance statistics so you can get a sense for how long a
simulation will take, and how much memory will be required for various
population sizes and sequence lengths.

Happy Simulating!!

Ryan