states of the internal nodes

[computingmachine]

Can the simulator output the states of the internal nodes instead of the tips only?

[dapogon]

Yes, see section 6.5 of the manual:

5: print MRCA sequences

Prints genotypes/haplotypes also for the sample MRCA and sample/outgroup MRCA (see Fig. 3).

On Thu, Sep 3, 2020 at 8:59 PM Yuan Gao notifications@github.com wrote:

Can the simulator output the states of the internal nodes instead of the tips only?

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[computingmachine]

The -5 option output the states of the MRCA, can cellcoal output the states of all internal nodes? Here is the code I used

bin/cellcoal-1.1.0 -n5 -s10 -l1000 -e10000 -g0.001 -k0 -q0 -i1 -b0 -u1.0e-07 -m2-p0.0 -G0.4 0.23999 -1 -2 -3 -4 -5 -6 -9 -oresults -v -#200011

For example, in figure 3, the states of node linking cell 1 and cell 2 is unknown.

[dapogon]

Ok, I can do this for the next release, d

On Fri, Sep 4, 2020 at 5:39 PM Yuan Gao notifications@github.com wrote:

The -5 option output the states of the MRCA, can cellcoal output the states of all internal nodes? Here is the code I used

bin/cellcoal-1.1.0 -n5 -s10 -l1000 -e10000 -g0.001 -k0 -q0 -i1 -b0 -u1.0e-07 -m2-p0.0 -G0.4 0.23999 -1 -2 -3 -4 -5 -6 -9 -oresults -v -#200011

For example, in figure 3, the states of node linking cell 1 and cell 2 is unknown.

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[computingmachine]

OK, that sounds great! When the next version is expected to release?

[dapogon]

well, if not relevant bugs appear, it might take a while, depending on the growing list of potential changes and time availability (this semester will be complicated)

On Fri, Sep 4, 2020 at 9:16 PM Yuan Gao notifications@github.com wrote:

OK, that sounds great! When the next version is expected to release?

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-- David Posada CINBIO Universidade de Vigo 36310 Vigo Spain

Phone: +34 986 812038 Cell: +34 647 343300 Fax: +34 986 812556 Email: dposada@uvigo.es Web: http://darwin.uvigo.es

[computingmachine]

I see. Thanks! Looking forward to the update!

On Mon, Sep 7, 2020 at 5:33 AM David Posada notifications@github.com wrote:

well, if not relevant bugs appear, it might take a while, depending on the growing list of potential changes and time availability (this semester will be complicated)

On Fri, Sep 4, 2020 at 9:16 PM Yuan Gao notifications@github.com wrote:

OK, that sounds great! When the next version is expected to release?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/dapogon/cellcoal/issues/2#issuecomment-687332862, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AE4VEERWWSXQC72IFI2IYR3SEE4JBANCNFSM4QVPAKHA

.

-- David Posada CINBIO Universidade de Vigo 36310 Vigo Spain

Phone: +34 986 812038 Cell: +34 647 343300 Fax: +34 986 812556 Email: dposada@uvigo.es Web: http://darwin.uvigo.es

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