contiguous ancestral regions (CARs) too small

[zhangzhiyangcs]

contiguous ancestral regions (CARs) too small

[DyogenIBENS]

Hello,
depending of the local rearrangements on each descendant species, AGORA will do its best to detect ancestral continuity.
To reconstruct the N0 ancestor of these 3 species (that I guessed are plants, in which occurred a recent whole genome duplication if they are solenacea), you may add more species, and probably outgroups. To linearize ancestral graphs, the algorithm needs more information en edges to choose the good adjacency in case of bifurcations, or will prefer to break the linearization.
Moreover, can I ask you what algorithm has been used? agora-basic or agora-plants ?
Best,
Alexandra

[zhangzhiyangcs]

Hi,
Thanks your advice, I try the agora-plants which is better than agora-basic methods. In my study, I want to reconstruct the ancestor assembly of tomato and eggplant based on recently published assemblies. There are some assemblies didn't reach to chromosome-level with N50 about 5Mb. Should I order them to chromosome-level assembly first? And if I add the outgroups such as Convolvulaceae which is relative to the Solanaceae and the number assemblies of tomato and eggplant (nearly 40 assemblies). will it work for construction of better ancestor assemblies.

Besides, there is little question. My species tree is (((Capsicum_chinense.pep:0.0252409,Capsicum_annuum.pep:0.0240399)N3:0.0175153,Capsicum_baccatum.pep:0.0282492)N1:0.0466179,((Solanum_melongena.pep:0.0746262,Solanum_stramoniifolium.pep:0.0471138)N4:0.0307135,(Solanum_septemlobum.pep:0.0572046,((S_habrochaites.pep:0.0373641,((S_peruvianum.pep:0.00923837,S_corneliomulleri.pep:0.0115695)N12:0.00782262,((S_chmielewskii.pep:0.00604881,S_neorickii.pep:0.00387453)N16:0.00643749,((TS112.pep:0.000391208,(TS12.pep:0.000455136,(TS166.pep:0.000311636,(TS171.pep:0.000462916,(TS185.pep:0.00132264,((TS222.pep:0.00165556,(TS281.pep:0.000662984,(TS3.pep:0.000966943,(TS331.pep:0.00122259,(TS39.pep:0.00134176,(TS413.pep:0.00293421,(TS421.pep:0.00251827,(TS60.pep:0.000387697,(TS623.pep:0.00124921,(TS629.pep:0.000523416,(TS692.pep:0.000930574,(TS80.pep:0.00125964,(TS96.pep:0.00185362,TS9.pep:0.000536475)N88:0.000241379)N87:5.16774e-05)N86:1.4978e-10)N85:1.41343e-06)N84:0)N83:1.41343e-06)N81:1.41343e-06)N79:1.41343e-06)N77:0)N75:0)N71:0)N63:0)N57:0,TS204.pep:0.00104421)N51:0)N46:1.41343e-06)N40:0)N33:0)N26:1.41343e-06)N21:1.41343e-06,(((PI303721.pep:0.000793696,PI169588.pep:0.00105927)N34:0.00377143,(MM.pep:0.000631467,(LYC1410.pep:0.000602446,(LA2093.pep:0.00362734,((Fla8924.pep:0.000702611,(EA00990.pep:0.000730518,(EA00371.pep:0.000815361,((BGV007989.pep:0.000645467,(BGV007931.pep:0.00169789,(BGV006775.pep:0.00202178,BGV006865.pep:0.00315751)N82:0.000416142)N80:1.70643e-05)N78:2.28092e-08,Brandywine.pep:0.000949199)N76:7.4813e-11)N72:6.72043e-11)N64:1.41343e-06)N58:2.92826e-11,Floradade.pep:0.000640548)N52:3.0303e-11)N47:4.03226e-11)N41:4.20168e-11)N35:4.24628e-11)N27:0,(PP.pep:0.00287131,PAS014479.pep:0.00307313)N28:0.00463748)N22:0)N17:0.0100754)N13:0.0046876)N9:0.00865879)N7:0.0269158,((ETB_C347:0.0131824,ETB_C351:0.0185872)N10:0.0218274,((C514:0.0275098,((C447:0.015782,C356:0.0169236)N23:0.00968925,C656:0.0234373)N18:0.00588131)N14:0.00647229,((((C450:0.0191488,C390:0.0176664)N29:0.00763655,((C522:0.0176182,C369:0.018946)N36:0.0101215,C813:0.0187475)N30:0.00628604)N24:0.00542426,C361:0.0198491)N19:0.00645283,(C550:0.0209802,((((C031:0.0070568,C580:0.0136637)N42:0.00884751,(((C574:0.0130549,C399:0.0127784)N53:0.00867931,(C419:0.00876492,C454:0.00974861)N54:0.00575909)N48:0.00534487,(((C337:0.00969067,C115:0.00714451)N59:0.00796747,((C426:0.00437438,DM_best.pep:0.00426467)N65:0.00226081,((C118:0.00582822,C058:0.00455901)N73:0.00635447,(C190:0.00387392,C219:0.00716368)N74:0.00488972)N66:0.00443546)N60:0.00380564)N55:0.00451725,(((C005:0.00609156,C098:0.00656238)N67:0.00502117,(C151:0.00537252,C174:0.00584118)N68:0.00467373)N61:0.0113463,((A157:0.00431011,C001:0.00521146)N69:0.00132905,(C056:0.0068361,C093:0.00630395)N70:0.00699816)N62:0.000614525)N56:1.199e-05)N49:0.00804961)N43:0.00594414)N37:0.00158365,(C373:0.0174046,C382:0.0154129)N38:0.00976102)N31:0.00353089,((((C408:0.0121938,C533:0.0108567)N50:0.00635865,C872:0.0138205)N44:0.0044298,(C554:0.0128995,C552:0.0140432)N45:0.00610672)N39:0.00570481,C559:0.0216849)N32:0.0035472)N25:0.00636359)N20:0.00580869)N15:0.00582276)N11:0.00767319)N8:0.0088454)N6:0.0263617)N5:0.0138781)N2:0.0466179)N0.

If I only care about N53 ancestor assemblies. Is there a parameters that help me omit the preparation of other orthologyGroups.%s.list.bz2 and genes.%s.list.bz2 files.

[muffato]

Hi @zhangzhiyangcs

Generally speaking, the more species you give AGORA, the better the reconstructions will be. If you only want to reconstruct the N53 ancestor, add -target==N53 to the command-line (make sure you run on the latest dev branch as I have fixed a bug about this option: #8)

Best,
Matthieu