scrm.github.io

Next-Gen Coalescent Simulation

Is a coalescent simulator for biological sequences. Different to similar programs, it can approximate the Ancestral Recombination Graph as closely as needed, but still has only linear runtime cost for long sequences. It allows you to rapidly simulate chromosome scale sequences with essentially correct genetic linkage. 10 Apr 2016: Version 1.7.2 Released. 23 Mar 2016: Version 1.7.1 Released. 07 Feb 2016: Version 1.7.0 Released. 09 Jul 2015: Version 1.6.1 Released. Scrm v1.7.2. In R to install it.

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Next-Gen Coalescent Simulation | scrm.github.io Reviews

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Is a coalescent simulator for biological sequences. Different to similar programs, it can approximate the Ancestral Recombination Graph as closely as needed, but still has only linear runtime cost for long sequences. It allows you to rapidly simulate chromosome scale sequences with essentially correct genetic linkage. 10 Apr 2016: Version 1.7.2 Released. 23 Mar 2016: Version 1.7.1 Released. 07 Feb 2016: Version 1.7.0 Released. 09 Jul 2015: Version 1.6.1 Released. Scrm v1.7.2. In R to install it.

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Next-Gen Coalescent Simulation | scrm.github.io Reviews

https://scrm.github.io

Is a coalescent simulator for biological sequences. Different to similar programs, it can approximate the Ancestral Recombination Graph as closely as needed, but still has only linear runtime cost for long sequences. It allows you to rapidly simulate chromosome scale sequences with essentially correct genetic linkage. 10 Apr 2016: Version 1.7.2 Released. 23 Mar 2016: Version 1.7.1 Released. 07 Feb 2016: Version 1.7.0 Released. 09 Jul 2015: Version 1.6.1 Released. Scrm v1.7.2. In R to install it.

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scrm.github.io

1

Version 1.6.0 Released

http://scrm.github.io/release/Version-1.6.0-released.html

Version 1.6.0 Released. Version 1.6.0 was released today. Changes:. It is now possible to specify the approximation exact window in number of recombination events (#73). Scrm now uses a conservative approximation by default (#75). Critical: Position based rates changes (. Were only applied to the first locus. If. Was greater than one, all other loci were simulated with the rates from the end of the first one (#74). All simulations done with previous versions that used. Greater than one should be repeated.

2

Version 1.7.0 Released

http://scrm.github.io/release/Version-1.7.0-released.html

Version 1.7.0 Released. It has been a while since scrm 1.6.1 was released. We finally released the new version 1.7.0 today. It brings the ‘ transpose-segsites’ command line flag which prints the segregating sites with rows repesenting mutations instead of individuals and contains some additional information about the mutations. Scrm now throws an error when mutation or recombination rate changes have invalid sequence positions (#82). Has not set to. Fixes scrm’s tests suite on 32 bit systems (#98).

3

News

http://scrm.github.io/archive.html

April 10, 2016. Raquo; Version 1.7.2 Released. March 23, 2016. Raquo; Version 1.7.1 Released. February 7, 2016. Raquo; Version 1.7.0 Released. July 9, 2015. Raquo; Version 1.6.1 Released. June 4, 2015. Raquo; Version 1.6.0 Released. May 18, 2015. Raquo; Version 1.5.1 Released. April 7, 2015. Raquo; Version 1.5.0 Released. April 4, 2015. Raquo; Version 1.4.1 Released. March 29, 2015. Raquo; Version 1.4.0 Released. January 9, 2015. Raquo; Paper Published. December 23, 2014. Raquo; Paper Accepted.

4

Version 1.7.2 Released

http://scrm.github.io/release/Version-1.7.2-released.html

Version 1.7.2 Released. We just published another bug-fix update, version 1.7.2. The new version fixes another problem related to the. Option (#104). In previous version,. Could sometimes abort simulation using this option, and throw a number of different error messages. Laquo; Version 1.7.1 Released.

5

Version 1.6.1 Released

http://scrm.github.io/release/Version-1.6.1-released.html

Version 1.6.1 Released. Version 1.6.1 was released today. Changes:. Scrm had extensive memory consumption when simulating trees in large models (#79). This is now fixed, it is however no longer possible to use -O and -T at the same time. Laquo; Version 1.6.0 Released. Version 1.7.0 Released ».

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paulstaab.de

paulstaab.de - Science

http://paulstaab.de/./science

Coala: An R framework for coalescent simulation. Paul R. Staab and Dirk Metzler. Co-estimation of Demography and Positive Selection. Paul R. Staab. Scrm: efficiently simulating long sequences using the approximated coalescent with recombination. Paul R. Staab, Sha Zhu, Dirk Metzler, and Gerton Lunter. Bioinformatics 31 (10), 1680-1682. Why to account for finite sites in population genetic studies and how to do this with Jaatha 2.0. Ecology and Evolution (2013). Muller’s ratchet with compensatory mutations.

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scrm.github.io

Next-Gen Coalescent Simulation

Is a coalescent simulator for biological sequences. Different to similar programs, it can approximate the Ancestral Recombination Graph as closely as needed, but still has only linear runtime cost for long sequences. It allows you to rapidly simulate chromosome scale sequences with essentially correct genetic linkage. 10 Apr 2016: Version 1.7.2 Released. 23 Mar 2016: Version 1.7.1 Released. 07 Feb 2016: Version 1.7.0 Released. 09 Jul 2015: Version 1.6.1 Released. Scrm v1.7.2. In R to install it.

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