[phylocom-user] FW: Phylocom Problem - nodesig and nodesigl

Cam Webb cam_webb at yahoo.com
Mon May 22 12:13:59 PDT 2017


Dear Astrid,

I think the answer is that different runs of both `nodesig` and `nodesigl` will produce different results depending on the unique randomization results of a particular run.  You can see this by running:

  phylocom nodesigl -f Tree50_test.txt -s sample50_test.txt -t dummy.traits | grep + | wc

  phylocom nodesig -f Tree50_test.txt -s sample50_test.txt -t dummy.traits | grep -o SIGMORE | wc

Both output formats will sometimes give 6 SIGMOREs, sometimes 7. So it just happened that you got 7 when you ran `nodesig` and 6 when you ran `nodesigl`.  Doing more runs (e.g., with `-r 99999) stabilizes the output at 6 SIGMOREs.

Best,

Cam




> Astrid Henz Ryen wrote on 2017-05-22:
> 
> Hi all,
>
> I am using the commands nodesig and nodesigl to calculate some "hotnodes".
> I have some test files to learn how to do it and discovered that I get
> different results regarding the marked nodes.
>
> I found this post from a few years ago "Phylocom Problem” (Jul 2013) -
> a similar problem apparently. Has there been an answer or was the
> problem solved?
>
> Otherwise, I have some simple test files that give me the following: 
> When I run the command nodesig (in the shell), the resulting nexus
> file has 7 nodes that are marked [%note = 'string:SIGMORE']. The
> command nodesigl gives me the table where significant nodes are marked
> with "+". However, in the table, there are only 6 nodes marked with
> "+" - so one node signal less!
>
> With other data I also encountered the opposite: the nexus file has
> less nodes marked with [%note = 'string:SIGMORE’] and the table from
> nodesigl has more nodes marked with “+”.
>
> So what could be the problem? The numbers should match, or do [%note =
> 'string:SIGMORE’] and “+” actually mean different things?
> Appended you will find my test files. 
>
> Thank you in advance! 
>
> Astrid
>
> ((((t10:0.08483498031,t19:0.4301223764)n54:0.4631485674,t13:0.2320648963)n53:0.794106452,t2:0.2164290501)n52:0.9080718642,((((t37:0.6943789334,t38:0.7461413804)n58:0.3076319057,(((t25:0.2159007729,t26:0.6960813459)n61:0.9582526763,(((t28:0.8584941821,((t15:0.545571439,t44:0.8833270352)n66:0.5968560949,t50:0.1252796885)n65:0.4291080588)n64:0.6524661051,(t14:0.366440149,(t7:0.553638906,t34:0.2490988935)n68:0.06200060295)n67:0.159533445)n63:0.7032217034,(((((t6:0.7804590599,(t30:0.3484495264,t1:0.9896114354)n74:0.4730198444)n73:0.7117501746,t3:0.9746575775)n72:0.1462890762,(t48:0.2562978147,t46:0.4380919901)n75:0.1023208827)n71:0.2363639225,((t17:0.009650637396,t45:0.410664048)n77:0.9391639882,((t47:0.2431057948,t18:0.7678920524)n79:0.7232320921,(t23:0.3130610243,((t4:0.1089228119,t24:0.6276486197)n82:0.8204102572,((t12:0.4440983194,(t11:0.4581185298,t36:0.03998835338)n85:0.7824272343)n84:0.01476749219,(t42:0.7721325823,t5:0.8922508701)n86:0.339831776)n83:0.9205575543)n81:0.3126579856)n80:0.8510469834)n78:0.5689904899)n76:0.4497250214)n70:0.6185410917,t31:0.2823930355)n69:0.3816880439)n62:0.02085431106)n60:0.09242215636,(t35:0.6268108939,(t43:0.1006306263,(t16:0.2167906952,(t33:0.8100671028,t27:0.6262247979)n90:0.09140545037)n89:0.5031323978)n88:0.03147847694)n87:0.1132384718)n59:0.4039292808)n57:0.9786730357,(((t21:0.9744197447,t22:0.8259064641)n93:0.03859359096,(t9:0.4418640139,t39:0.5239426487)n94:0.6308366193)n92:0.8261045758,(t49:0.1726470103,(t29:0.4010839756,t41:0.565899339)n96:0.804941776)n95:0.5485613956)n91:0.2316776423)n56:0.6082377711,(t32:0.9624488796,((t40:0.5165954623,t20:0.1620237159)n99:0.673833966,t8:0.05191156757)n98:0.02774125896)n97:0.7568685969)n55:0.2002127783)n51;
>
>
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