Submit Computation Job

Upload genome files and configure analysis parameters

Example Input Files

Example files for your submissions (details in the respective sections below):

species.txt (NCBI Accessions)

GCF_000001215.4
GCF_009193385.2

genmap_params.txt

GCF_000001215.4 14 0 700 100 30 0
GCF_000001215.4 14 0 700 100 60 1
GCF_009193385.2 14 0 700 100 30 0
GCF_009193385.2 14 0 700 100 60 1

macle_params.txt

GCF_000001215.4 2000 200 30 0
GCF_000001215.4 2000 200 60 1
GCF_009193385.2 1000 200 30 0
GCF_009193385.2 1000 200 60 1

dups_params.txt

GCF_000001215.4 100 2 15 0 300 50 11 95 15 15
GCF_009193385.2 100 2 15 0 300 50 11 95 15 15

Note: Example results are in Sets as "{some_job_uuid}-example_output". Download anchors from the Species table.

Job Information

Email is optional. If provided, you'll receive notifications when your job completes.

Species Selection

Select species with pre-computed anchors to combine with your uploaded data.

You can select species here AND upload txt/fasta files below - they will be combined. Or use this as your only input (2+ species required).
Select Species Name Genome Source NCBI ID Last Job
Abia candens NCBI GCA_964212075.1 created_14a3f68b
Abraxas sylvata NCBI GCA_964187985.1 created_124a88b1
Acanthacorydalis orientalis NCBI GCA_034766995.1 job_ff2372e0
Acanthacorydalis orientalis NCBI GCA_034766995.1 created_3dc8af64
Acanthococcus lagerstroemiae NCBI GCA_031841125.1 created_252192b8
Achelura yunnanensis NCBI GCA_041274885.1 job_ff2372e0
Achelura yunnanensis NCBI GCA_041274885.1 created_babb96cb
Achlya flavicornis NCBI GCA_947623365.1 created_93300913
Acleris cristana NCBI GCA_948252455.1 created_91bfcbf3
Acleris holmiana NCBI GCA_949316455.1 created_857707a0
Acleris laterana NCBI GCA_963966035.1 created_d276ab08
Acleris literana NCBI GCA_946894065.1 created_24beb42e
Acleris sparsana NCBI GCA_923062465.1 created_547aac58
Acrobasis repandana NCBI GCA_963576875.1 created_642d07d0
Acrobasis suavella NCBI GCA_943193695.1 created_52db9f90
Acrocera orbiculus NCBI GCA_947359355.1 created_36155bcb
Acronicta aceris NCBI GCA_910591435.1 created_7a125a77
Acronicta alni NCBI GCA_964056405.1 created_6c853e84
Acronicta leporina NCBI GCA_947256265.1 created_e0c60e31
Actenicerus siaelandicus NCBI GCA_964234755.1 created_2ee4254c
Acyrthosiphon pisum NCBI GCF_005508785.2 created_a0442550
Adalia bipunctata NCBI GCA_910592335.1 created_d249b266
Adalia decempunctata NCBI GCA_951802165.1 created_7aab6758
Adelphocoris suturalis NCBI GCA_030762985.1 created_917895bc
Aedes aegypti NCBI GCF_002204515.2 created_ad98c45c
Aedes aegypti aegypti NCBI GCA_025407655.1 created_628303d1
Agriopis leucophaearia NCBI GCA_949125355.1 created_55ce2949
Aleiodes testaceus NCBI GCA_963565655.1 created_02867ac6
Alloascoidea hylecoeti NCBI GCA_001600815.1 created_2f65e1f4
Alloplasta piceator NCBI GCA_946863875.1 created_90fbd355
Ametastegia equiseti NCBI GCA_963989295.1 created_c0f35d02
Anania hortulata NCBI GCA_963576865.1 created_2d395db1
Andrena praecox NCBI GCA_963932275.1 created_6d6be80d
Anopheles aquasalis NCBI GCF_943734665.1 created_1c3769ab
Anopheles longipalpis NCBI GCA_016170015.1 created_90ff9cb1
Anopheles ziemanni NCBI GCF_943734765.1 created_675c5cfd
Anoplius nigerrimus NCBI GCA_914767735.1 created_b5ef0d3c
Anthonomus grandis thurberiae NCBI GCA_030068095.1 created_453727f8
Aphodius fimetarius NCBI GCA_964211865.1 created_d1105f22
Aplocera praeformata NCBI GCA_964260645.1 created_128d5f52
Araneus marmoreus NCBI GCA_050042785.1 created_09c0507c
Argiope bruennichi NCBI GCF_947563725.1 created_b809f428
Athalia cordata NCBI GCA_963932425.1 created_50fda569
Athalia rosae NCBI GCF_917208135.1 created_de2c5342
Atherix ibis NCBI GCA_958298945.2 created_a75bf182
Athetis lepigone NCBI GCA_033675125.1 created_e40cccc8
Athrips mouffetella NCBI GCA_947532105.1 created_53d324c8
Athripsodes cinereus NCBI GCA_947579605.1 created_7b5b27f4
Augochlora pura NCBI GCA_028453695.1 created_21f42272
Augochlorella aurata NCBI GCA_028455555.1 created_1d65bb85
Autographa bractea NCBI GCA_964264225.1 created_d23ffc29
Autographa gamma NCBI GCA_905146925.1 created_b53bc00b
Autographa pulchrina NCBI GCA_905475315.1 created_66e8b46d
Azelia nebulosa NCBI GCA_964235425.1 created_0020e500
Bactrocera neohumeralis NCBI GCF_024586455.1 created_4aa2f787
Bombus affinis NCBI GCF_024516045.1 created_8a2f2c91
Bombus fervidus NCBI GCA_041682495.1 created_3a533f95
Bombus pyrosoma NCBI GCF_014825855.1 created_666a0d7c
Bombus vestalis NCBI GCA_963556215.1 created_0b294f66
Bombylius major NCBI GCA_932526495.1 created_0fb129d2
Bombyx mori NCBI GCF_030269925.1 created_4f19dd26
Bombyx mori NCBI GCF_030269925.1 created_b3bd0c99
Buchnera aphidicola str. APS (Acyrthosiphon pisum) NCBI GCF_000009605.1 created_daddee8f
Caenorhabditis elegans NCBI GCF_000002985.6 test_many_orgs_1766579940
Caenorhabditis_angaria NCBI Caenorhabditis_angaria created_796cb653
Caenorhabditis_nigoni NCBI Caenorhabditis_nigoni created_e04a2ae4
Caenorhabditis_sinica NCBI Caenorhabditis_sinica created_968d2533
Candida albicans SC5314 NCBI GCA_000182965.3 created_5784a9ac
Candida dubliniensis CD36 NCBI GCA_000026945.1 created_b3cb0e60
Candida maltosa Xu316 NCBI GCA_000344705.1 created_76e232c1
Candida metapsilosis NCBI GCA_008904905.1 created_f68ef7a5
Candida orthopsilosis Co 90-125 NCBI GCA_000315875.1 created_38909495
Candida parapsilosis NCBI GCA_000182765.2 created_ca96bece
Candida sojae NCBI GCA_001442715.1 created_b79e020d
Candida sp. LDI48194 NCBI GCA_001005365.1 created_41a92f8e
Candida tropicalis MYA-3404 NCBI GCA_000006335.3 created_70862f2a
Cantharis flavilabris NCBI GCA_949152465.1 created_9589300a
Cerastis leucographa NCBI GCA_963082945.1 created_68effdc7
Chlorops oryzae NCBI GCA_020466095.1 created_9f486b6d
Cimex hemipterus NCBI GCA_039619505.1 created_06301540
Clepsis dumicolana NCBI GCA_963691665.1 created_19f97428
Condylostylus longicornis NCBI GCF_029603195.1 created_ea3f266c
Conogethes punctiferalis NCBI GCA_031163375.1 created_24e29731
Cosmorhoe ocellata NCBI GCA_963675405.1 created_e2dddf98
Culicoides brevitarsis NCBI GCF_036172545.1 created_460fe3fd
Cylindricascospora bacillisporus CBS 7720 NCBI GCA_001046975.1 created_03986748
Debaryomyces fabryi NCBI GCA_001447935.1 created_2f1e8697
Debaryomyces hansenii CBS767 NCBI GCA_000006445.2 created_b7823069
Diorhabda sublineata NCBI GCF_026230105.1 created_8a549158
Diprion similis NCBI GCF_021155765.1 created_4ab5cb59
Drosophila albomicans NCBI GCF_009650485.2 created_0caeb94d
Drosophila ananassae NCBI GCF_017639315.1 tut_scaff
Drosophila ananassae NCBI GCA_018148915.1 created_91e79408
Drosophila ananassae NCBI GCF_017639315.1 created_34d2cbdf
Drosophila biarmipes NCBI GCA_018148935.1 created_daff99be
Drosophila bipectinata NCBI GCA_030179905.1 created_fa6c705f
Drosophila bipectinata NCBI GCA_021223765.1 created_4f8f3692
Drosophila burlai NCBI GCA_008042655.1 created_c05f36bf
Drosophila busckii NCBI GCF_011750605.1 created_7c4aa7fb
Drosophila busckii NCBI GCF_011750605.1 created_73dfa0f9
Drosophila elegans NCBI GCF_018152505.1 created_1fca7edb
Drosophila erecta NCBI GCA_018904525.1 created_966c54d7
Drosophila eugracilis NCBI GCF_018153835.1 tut_scaff
Drosophila eugracilis NCBI GCF_018153835.1 created_048f6989
Drosophila eugracilis NCBI GCF_018153835.1 created_6955de6a
Drosophila ficusphila NCBI GCF_018152265.1 created_8a71bcb8
Drosophila kikkawai NCBI GCF_030179895.1 tut_scaff
Drosophila kikkawai NCBI GCF_030179895.1 created_22b472a4
Drosophila kikkawai NCBI GCA_018152535.1 created_c2a8f17e
Drosophila malerkotliana malerkotliana NCBI GCA_018153235.1 created_48c01bb0
Drosophila mauritiana NCBI GCA_018904475.1 created_a25c87f3
Drosophila melanogaster NCBI GCF_000001215.4 tut_scaff
Drosophila melanogaster NCBI GCF_000001215.4 created_ba549f99
Drosophila melanogaster NCBI GCF_000001215.4 created_f95951f2
Drosophila melanogaster NCBI GCA_000778455.1 created_37997090
Drosophila orena NCBI GCA_005876975.1 created_c2487f89
Drosophila pallidifrons NCBI GCA_023558445.1 created_9a4af43f
Drosophila persimilis NCBI GCF_003286085.1 created_59ae6f5e
Drosophila persimilis NCBI GCF_003286085.1 created_d3bd989b
Drosophila pseudoobscura NCBI GCF_009870125.1 tut_scaff
Drosophila pseudoobscura NCBI GCF_009870125.1 created_6dac015f
Drosophila rhopaloa NCBI GCF_018152115.1 created_561f5e7c
Drosophila sechellia NCBI GCF_004382195.2 tut_scaff
Drosophila sechellia NCBI GCA_018904445.1 created_f045c7e3
Drosophila sechellia NCBI GCF_004382195.2 created_04ffdd5b
Drosophila simulans NCBI GCF_016746395.2 tut_scaff
Drosophila simulans NCBI GCF_016746395.2 created_441e4c93
Drosophila simulans NCBI GCA_039725655.1 created_c3b6c96c
Drosophila suzukii NCBI GCF_037355615.1 created_c148bcc5
Drosophila takahashii NCBI GCF_030179915.1 tut_scaff
Drosophila takahashii NCBI GCA_018152695.1 created_add958c6
Drosophila takahashii NCBI GCF_030179915.1 created_c1683777
Drosophila teissieri NCBI GCA_018903625.1 created_aeaec18c
Drosophila virilis NCBI GCF_030788295.1 tut_scaff
Drosophila virilis NCBI GCF_030788295.1 created_5182fc51
Drosophila willistoni NCBI GCF_018902025.1 tut_scaff
Drosophila willistoni NCBI GCF_018902025.1 created_d59b9097
Drosophila willistoni NCBI GCF_018902025.1 created_dacffc15
Drosophila yakuba NCBI GCF_016746365.2 tut_scaff
Drosophila yakuba NCBI GCF_016746365.1 created_4b0885ff
Drosophila yakuba NCBI GCA_018904385.1 created_38028f0e
Drosophila yakuba NCBI GCF_016746365.2 created_66f561d0
Ectoedemia decentella NCBI GCA_964235475.1 created_ce42c82a
Eilema depressum NCBI GCA_914767945.1 created_24530127
Epinotia demarniana NCBI GCA_945867215.1 created_54c5c15b
Epistrophe grossulariae NCBI GCA_929447395.1 created_49e69ae4
Episyrphus balteatus NCBI GCF_945859705.1 created_c5617117
Episyrphus balteatus NCBI GCF_945859705.1 created_7b613697
Erebia embla NCBI GCA_964271835.1 created_d528b452
Erebia palarica NCBI GCA_964035005.1 created_1079086c
Eremothecium coryli CBS 5749 NCBI GCA_000710315.1 created_a749f117
Eremothecium cymbalariae DBVPG#7215 NCBI GCA_000235365.1 created_378e7377
Eremothecium gossypii ATCC 10895 NCBI GCA_000091025.4 created_48e6d9a9
Escherichia coli str. K-12 substr. MG1655 NCBI GCF_000005845.2 test_many_orgs_1766579940
Eupeodes corollae NCBI GCF_945859685.1 created_51bc6a81
Eupeodes corollae NCBI GCF_945859685.1 created_15a5e9bd
Eupithecia inturbata NCBI GCA_963662085.1 created_8cfdb783
Eupithecia pulchellata NCBI GCA_963931895.1 created_92077c16
Galerucella nymphaeae NCBI GCA_963978555.1 created_b2d0633f
Galleria mellonella NCBI GCF_026898425.1 created_f6ce228d
Galleria mellonella NCBI GCF_026898425.1 created_bff3f670
Geotrupes spiniger NCBI GCA_959613385.1 created_743f5f06
Halictus quadricinctus NCBI GCA_028454245.1 created_02200e8d
Hanseniaspora valbyensis NRRL Y-1626 NCBI GCA_001664025.1 created_8f6e079c
Henningerozyma blattae CBS 6284 NCBI GCA_000315915.1 created_b743d0e6
Hermetia illucens NCBI GCF_905115235.1 created_2b0d746e
Hololepta plana NCBI GCA_963695495.1 created_0382d12f
Homo sapiens NCBI GCF_000001405.40 test_many_orgs_1766579940
Hylyphantes graminicola NCBI GCA_023701765.1 created_f27e027d
Hyposoter dolosus NCBI GCA_963921915.1 created_68cd005c
Idaea aversata NCBI GCA_907269075.1 created_c812dbe6
Kluyveromyces aestuarii NCBI GCA_003707555.1 created_4b30e13b
Kluyveromyces dobzhanskii NCBI GCA_003705805.2 created_d23f27b4
Kluyveromyces lactis NCBI GCA_000002515.1 created_6017c051
Kluyveromyces marxianus DMKU3-1042 NCBI GCA_001417885.1 created_92a1547c
Kluyveromyces wickerhamii UCD 54-210 NCBI GCA_000179415.1 created_68400bef
Lachancea dasiensis NCBI GCA_900074725.1 created_72e9daa7
Lachancea fermentati NCBI GCA_900074765.1 created_a89becd4
Lachancea kluyveri NRRL Y-12651 NCBI GCA_000149225.1 created_6c5f9029
Lachancea lanzarotensis NCBI GCA_000938715.1 created_99d391d7
Lachancea meyersii CBS 8951 NCBI GCA_900074715.1 created_1ce929ce
Lachancea mirantina NCBI GCA_900074745.1 created_7acffb52
Lachancea nothofagi CBS 11611 NCBI GCA_900074755.1 created_8518fb81
Lachancea sp. 'fantastica' NCBI GCA_900074735.1 job_9a3460b5
Lachancea sp. 'fantastica' NCBI GCA_900074735.1 created_8ff57314
Lachancea thermotolerans CBS 6340 NCBI GCA_000142805.1 created_b2e2744f
Lachancea waltii NCBI GCA_000167115.1 created_80a67672
Latrodectus elegans NCBI GCA_030067965.1 created_4c019f5d
Latrodectus hesperus NCBI GCA_037975125.2 created_080b18b8
Leguminivora glycinivorella NCBI GCF_023078275.1 created_627c4820
Leucoma salicis NCBI GCA_948253155.1 created_a5fd9e67
Leviellus thorelli NCBI GCA_965183905.1 created_cf4f401c
Limenitis camilla NCBI GCA_905147385.1 created_c5c3c1d5
Lithophane socia NCBI GCA_947522985.1 created_839cceeb
Lodderomyces elongisporus NRRL YB-4239 NCBI GCA_000149685.1 created_1809bafb
Lomographa temerata NCBI GCA_964199915.1 created_7da61906
Lucilia cuprina NCBI GCF_022045245.1 created_111981e2
Lucilia cuprina NCBI GCF_022045245.1 created_457990ef
Malacosoma alpicolum NCBI GCA_964270795.1 created_dd74258b
Marasmia exigua NCBI GCA_019059595.1 created_7e544353
Megamerina dolium NCBI GCA_963854835.1 created_d5cf7309
Merzomyia westermanni NCBI GCA_949987695.1 created_b8407f01
Metellina segmentata NCBI GCA_947359465.1 job_9a3460b5
Monochamus alternatus NCBI GCA_037114965.1 created_5a2d78b8
Musca vetustissima NCBI GCF_032173495.1 created_adcbe0db
Musca vetustissima NCBI GCF_032173495.1 created_4a887a3c
Mycoplasmoides genitalium G37 NCBI GCF_000027325.1 created_b54a5954
Myopa testacea NCBI GCA_949629155.1 created_cd4a7819
Nakaseomyces bracarensis CBS 10154 NCBI GCA_001077315.1 created_1236b8f3
Nakaseomyces delphensis CBS 2170 NCBI GCA_001039675.1 created_dfab42b4
Nakaseomyces glabratus NCBI GCA_000002545.2 created_7be07617
Nakaseomyces nivariensis CBS 9983 NCBI GCA_001046915.1 created_239c1896
Nasonia vitripennis NCBI GCF_009193385.2 created_3fa61523
Naumovozyma castellii NCBI GCA_000237345.1 created_987406ec
Naumovozyma dairenensis CBS 421 NCBI GCA_000227115.2 created_0c90dd3e
Notodonta dromedarius NCBI GCA_905147325.1 created_6c7c1286
Nudaria mundana NCBI GCA_963556515.1 created_05d81b5b
Nycteola revayana NCBI GCA_947037095.2 created_891a75b2
Nylanderia fulva NCBI GCA_024268025.1 created_2872fccc
Octonoba sinensis NCBI GCA_038502835.1 created_00f6538c
Oedothorax gibbosus NCBI GCA_019343175.1 job_9a3460b5
Oedothorax gibbosus NCBI GCA_019343175.1 created_45c88c82
Ogataea parapolymorpha DL-1 NCBI GCA_000187245.3 created_1ca25811
Ogataea polymorpha NCBI GCA_001664045.1 created_4a22ba72
Oligophagozyma castellii CBS 4332 NCBI GCA_001046935.1 created_18479b99
Orthosia incerta NCBI GCA_948252205.1 created_51f235fa
Parasteatoda tepidariorum NCBI GCF_043381705.1 created_af4c30aa
Pardosa pseudoannulata NCBI GCA_032207245.1 created_93998f3a
Perizoma blandiatum NCBI GCA_964188255.1 created_045758eb
Philereme transversata NCBI GCA_963924445.1 created_b48fc2b2
Philonicus albiceps NCBI GCA_963969385.1 created_5938e7db
Phlebotomus argentipes NCBI GCF_947086385.1 created_9ca9baee
Phlebotomus argentipes NCBI GCF_947086385.1 created_b162f819
Phyto melanocephala NCBI GCA_941918925.1 created_9e479795
Polyommatus iphigenia NCBI GCA_963422495.1 created_4bf97153
Propylea japonica NCBI GCA_013421045.1 created_46c7d295
Pyrausta aurata NCBI GCA_963584085.1 created_238406cc
Pyrgus malvae NCBI GCA_911387765.1 created_d8ab283f
Pyrocoelia pectoralis NCBI GCA_036250285.1 created_ca8eec71
Rhodophaea formosa NCBI GCA_963082605.1 created_e8611048
Saccharomyces cerevisiae NCBI GCA_001413975.1 created_ed1e5d14
Saccharomyces cerevisiae S288C NCBI GCF_000146045.2 test_many_orgs_1766579940
Saccharomyces cerevisiae S288C NCBI GCA_000146045.2 created_571861d2
Saccharomyces cerevisiae x Saccharomyces kudriavzevii VIN7 NCBI GCA_000326105.1 created_1fd709bc
Saccharomyces eubayanus NCBI GCA_001298625.1 created_18881fc6
Saccharomyces kudriavzevii NCBI GCA_003327635.1 created_6f9e7944
Saccharomyces mikatae IFO 1815 NCBI GCA_000166975.1 created_6c757431
Saccharomyces paradoxus NCBI GCA_002079145.1 created_e8c126e4
Saccharomyces pastorianus Weihenstephan 34/70 NCBI GCA_001515485.2 created_a5827081
Saccharomyces sp. M14 NCBI GCA_002375215.1 created_d21d4f79
Saccharomyces uvarum NCBI GCA_002242645.1 created_418b5100
Saccharomyces uvarum CLIB 533 NCBI GCA_000167035.1 created_bfffdbbf
Sarcophaga caerulescens NCBI GCA_927399465.1 created_73612058
Sarcophaga variegata NCBI GCA_932273835.1 created_211717db
Scathophaga stercoraria NCBI GCA_040938175.1 created_b77b23d3
Selenia dentaria NCBI GCA_917880725.1 created_ef6e81a7
Sesamia inferens NCBI GCA_037179545.1 created_3b6a4c7a
Sitodiplosis mosellana NCBI GCA_021018905.1 created_889ee822
Sitona lineatus NCBI GCA_964263205.1 created_7cab3041
Slavum lentiscoides NCBI GCA_032441835.1 created_c20ed3aa
Smittia aterrima NCBI GCA_033063855.1 created_272a0182
Smittia sp. YW1114-2 NCBI GCA_033064975.1 created_966d5798
Sogatella furcifera NCBI GCA_017141385.1 created_c881ead7
Solenopsis invicta NCBI GCF_016802725.1 created_c1df8f75
Sphaerophoria taeniata NCBI GCA_943590905.1 created_2ec51d9c
Sphecodes monilicornis NCBI GCA_913789915.3 created_918c6e25
Spilarctia lutea NCBI GCA_916048165.1 created_764a8552
Spilosoma urticae NCBI GCA_964188045.1 created_16d56c29
Spodoptera exigua NCBI GCA_902829305.4 created_0ab74b0a
Spodoptera frugiperda NCBI GCF_011064685.2 created_5e315491
Spodoptera littoralis NCBI GCA_902850265.1 created_1cd54838
Spodoptera litura NCBI GCF_002706865.2 created_897723aa
Standfussiana lucernea NCBI GCA_964057025.1 created_1d5ea19e
Staphylinus erythropterus NCBI GCA_964211955.1 created_473023fe
Stegodyphus bicolor NCBI GCA_044657725.1 created_3b618f21
Stegodyphus lineatus NCBI GCA_044657705.1 created_4142196c
Stenchaetothrips biformis NCBI GCA_030522485.1 created_7a618f03
Stenodema calcarata NCBI GCA_963920205.1 created_353da0d5
Stomorhina lunata NCBI GCA_933228675.1 created_3dbc0acc
Stratiomys singularior NCBI GCA_954870665.1 created_f3d7e77b
Sylvicola cinctus NCBI GCA_963854165.1 created_068c324f
Syritta pipiens NCBI GCA_905187475.1 created_705e4654
Tenthredo mesomela NCBI GCA_943736025.1 created_7fdde618
Thecocarcelia acutangulata NCBI GCA_914767995.1 created_eb094c5e
Thermotoga maritima MSB8 NCBI GCF_000008545.1 created_82384d34
Torulaspora delbrueckii NCBI GCA_000243375.1 created_aa68f63a
Torulaspora microellipsoides NCBI GCA_900186055.1 created_7feead29
Tribolium castaneum NCBI GCF_031307605.1 created_f6c7dd61
Tribolium castaneum NCBI GCF_031307605.1 created_edcc3f18
Vespa velutina NCBI GCF_912470025.1 created_f6ba5f28
Villa cingulata NCBI GCA_951394055.1 created_67b72cc7
Zygaena carniolica NCBI GCA_964261665.1 created_897a7dcd
Zygosaccharomyces bailii CLIB 213 NCBI GCA_000442885.1 created_190e8ab9
Zygosaccharomyces parabailii NCBI GCA_001984395.2 created_4c8aaaea
Zygosaccharomyces rouxii NCBI GCA_000026365.1 created_679208fe
[Ashbya] aceris (nom. inval.) NCBI GCA_000412225.2 created_9f7c49c1
name not resolved NCBI GCA_963932265.1 created_8f893b94
name not resolved NCBI dee0396f-f6ba-4ef8-b178-1cfd2589e381_GCF_018153835.1_scaffolded scaff_lim
name not resolved NCBI dee0396f-f6ba-4ef8-b178-1cfd2589e381_GCF_018153835.1_scaffolded_limited scaff_lim
name not resolved NCBI 24aa4c8f-1f8a-4be4-bb08-1f51166d2d9b_GCF_018153835.1_scaffolded tut_scaff
name not resolved NCBI GCA_933210815.1 created_a51f06c6
name not resolved NCBI GCA_964059485.1 created_b139164f
name not resolved NCBI Solanum_pimpinellifolium created_a2be1b13
name not resolved NCBI Solanum_dulcamara created_33bac147
name not resolved NCBI Solanum_retroflexum created_812d4f42
name not resolved NCBI GCA_963978545.1 created_4c805dc7
name not resolved NCBI GCA_947359465.1 created_dd9d6484
name not resolved NCBI GCA_951213105.1 created_493e7307
name not resolved NCBI Capsicum_annuum created_1baacdcf
name not resolved NCBI Solanum_tuberosum created_1c895599
name not resolved NCBI Solanum_pseudocapsicum created_89b9ccb2
name not resolved NCBI Solanum_lyratum created_4db277bc
name not resolved NCBI Solanum_torvum created_0523a423
name not resolved NCBI Solanum_lycopersicum created_0c45e2af
name not resolved NCBI Solanum_viarum created_502f476e
name not resolved NCBI Solanum_candolleanum created_24c7ed3f
name not resolved NCBI Solanum_laciniatum created_4c4012de
name not resolved NCBI Solanum_galapagense created_c286e336
name not resolved NCBI Solanum_melongena created_5b630bb3
name not resolved NCBI Solanum_americanum created_8f0a0b23
name not resolved NCBI Solanum_spirale created_b0b97cb5
name not resolved NCBI GCA_946251955.1 created_010dc12b
name not resolved NCBI GCA_930367205.1 created_a51e8d45
name not resolved NCBI Solanum_pinnatisectum created_98e88ab7
name not resolved NCBI GCA_964197645.1 created_41bf5e3e
name not resolved NCBI GCA_927399475.2 created_f1a2046f
name not resolved NCBI GCA_943735885.1 created_4764366d
name not resolved NCBI GCA_964017025.1 created_780e4e72
name not resolved NCBI GCA_963555685.1 created_b769555e
name not resolved NCBI GCA_946251915.1 created_e424f6db
name not resolved NCBI Caenorhabditis_zanzibari created_49957295
name not resolved NCBI Caenorhabditis_latens created_cd96ccb8
name not resolved NCBI Caenorhabditis_inopinata created_2a1c6691
name not resolved NCBI Caenorhabditis_kamaaina created_7d3671b6
name not resolved NCBI Caenorhabditis_virilis created_a1bca56f
name not resolved NCBI Caenorhabditis_elegans created_7b6fc868
name not resolved NCBI Caenorhabditis_afra created_1f3b564b
name not resolved NCBI Caenorhabditis_tropicalis created_27c9ac4a
name not resolved NCBI Caenorhabditis_macrosperma created_7f73d709
name not resolved NCBI Caenorhabditis_wallacei created_6ecc09ff
name not resolved NCBI Caenorhabditis_drosophilae created_e1023a19
name not resolved NCBI Caenorhabditis_astrocarya created_d0612fbd
name not resolved NCBI Caenorhabditis_brenneri created_e621fd6f
name not resolved NCBI Caenorhabditis_plicata created_f901814f
name not resolved NCBI Caenorhabditis_parvicauda created_0924eaba
name not resolved NCBI Caenorhabditis_becei created_c7948305
name not resolved NCBI Caenorhabditis_monodelphis created_f06e40ad
name not resolved NCBI Caenorhabditis_sulstoni created_019f7922
name not resolved NCBI Caenorhabditis_dolens created_c8f85731
name not resolved NCBI Caenorhabditis_imperialis created_ae6f2d48
name not resolved NCBI Caenorhabditis_uteleia created_7c761dcf
name not resolved NCBI Caenorhabditis_quiockensis created_690cd25d
name not resolved NCBI Caenorhabditis_briggsae created_4d54a86b
name not resolved NCBI Caenorhabditis_agridulce created_5ef3adab
name not resolved NCBI Caenorhabditis_doughertyi created_8a651eac
name not resolved NCBI GCA_905340225.1 created_f9884502
name not resolved NCBI Caenorhabditis_japonica created_0a585798
name not resolved NCBI Caenorhabditis_waitukubuli created_65240eb6
name not resolved NCBI Caenorhabditis_remanei created_28f4b923

Genome Data

Upload files (optional if species selected above):

Input File Requirements

Input Options (choose one or combine):

  • NCBI Accessions file (.txt)
  • FASTA Genomes archive (.tar.gz)
  • Species from dropdown selection above
  • Any combination of the above

NCBI Accessions File (.txt):

  • Format: One accession per line
  • Valid examples: GCF_000001215.4, GCF_009193385.2

FASTA Archive Format (.tar.gz):

  • Extension: .tar.gz or .tgz
  • Must contain only FASTA files (.fasta, .fa, .fna, .fas)
  • FASTA file names (before extension) become species names
  • Example: genomes.tar.gz containing Escherichia_coli.fasta, Bacillus_subtilis.fasta

FASTA File Content Requirements:

  • Sequence ID: Max 25 characters, no spaces
  • Valid characters in ID: A-Z a-z 0-9 . _ : # * -
  • Individual genomes: Maximum 2.0 GB (raw/uncompressed size)

Example FASTA format:

Filename: Escherichia_coli.fasta
>genome_sequence_1
ATCGATCGATCG...

Note: Individual genome files must not exceed 2.0 GB (raw/uncompressed size). Jobs containing larger genomes will not be processed.

Note: Individual genomes downloaded from NCBI must not exceed 2.0 GB (raw/uncompressed size). Jobs containing larger genomes will not be processed.

Processing Options

Check this to only compute anchors for the submitted species without running the full synteny analysis. Useful for preparing data for future analyses.

Note about single-species submissions: When submitting only one species, pairwise alignments cannot be computed. Such submissions are automatically processed as anchor-only jobs, computing and storing anchors for future multi-species analyses. You will receive a downloadable archive containing the computed anchors.

Analysis Mode

Advanced Parameter Settings

Help with Parameters

Format for Advanced Parameter Settings:

- .txt files

Requirements

Parameter file requirements:

• Each species needs at least ONE of (genmap OR macle) parameters
• You can provide only genmap, only macle, or both
• Dups parameters are completely optional
• Automatic parameters are generated for any species missing both genmap and macle

Example scenarios:
✓ Upload only genmap.txt (macle auto-generated for species not in genmap.txt)
✓ Upload only macle.txt (genmap auto-generated for species not in macle.txt)
✓ Upload both genmap.txt and macle.txt
✓ Upload genmap.txt + dups.txt (macle auto-generated, dups optional)
✓ Upload nothing (all parameters auto-generated)

For all

Please provide line-separated files with a set of parameters according to the descriptions below. In short: genmap corresponds to filtering based on k-mer counting done with GenMap; macle corresponds to filtering done with macle, a tool to compute the match complexity; dups corresponds to identification of potential duplicates with the help of using longer k-mers with allowed errors for the detection of sequences with only few duplicates

At https://link.springer.com/article/10.1186/s13015-025-00275-9 the main paper describing the method can be found with a detailed description of the use of GenMap. The use of macle and the duplicate finding algorithm are subjects of the paper this webserver will be part of but a sufficient explanation is given below. If in doubt, dont use the duplicate finding mechanism. The macle tool is available on github and the parameters of window size and pitch should be straight forward.

genmap

The line is formatted like (whitespace in between):
genome k e w p s b
genome: filename without suffix (my_genome NOT my_genome.fa/fna/fasta)
k: k of k-mer counts
e: errors allowed in k-mer counting
w: size of initially overlapping windows
p: pitch of w-windows
s: (minimal) percentage of genome size of initially overlapping windows to process
b: value which one of [0,1]. 0 - take all windows. 1 - take only the ones overlapping with others from other genmap or macle filtering settings.

macle

The line is formatted like (whitespace in between):
genome w p s b
genome: filename without suffix (my_genome NOT my_genome.fa/fna/fasta)
w: size of initially overlapping windows
p: pitch of w-windows
s: (minimal) percentage of genome size of initially overlapping windows to process
b: value which one of [0,1]. 0 - take all windows. 1 - take only the ones overlapping with others from other genmap or macle filtering settings.

dups

The line is formatted like (whitespace in between):
genome k1 e1 k2 e2 w p x1 y1 x2 y2
genome: filename without suffix (my_genome NOT my_genome.fa/fna/fasta)
k1: k of k-mer counts for initial identification of candidate windows
e1: errors allowed in k1-mer counting
k2: k of k-mer counts for exclusion of windows according to x2 and y2
e2: errors allowed in k2-mer counting
w: size of initially overlapping windows
p: pitch of w-windows
x1: how many counts of initial windows are allowed (will be a range [2,x1])
y1: percentage of counts in candidate windows adhering to count values defined with x1
x2: how many counts of k2,e2-mers are regarded as indicative of bad window (and all bigger than x2)
y2: percentage of counts in candidate windows from which candidate is discarded if x2 count larger than to y2

Important Upload Information:
  • Large archive uploads may take several minutes to complete
  • You may see a timeout error in your browser even if the upload succeeded
  • If you receive a confirmation email with a Job ID, your upload was successful
  • Your job will be marked as "failed" or "genome_size_exceeded" only if:
    • The upload actually failed (no confirmation email)
    • Any individual genome exceeds 2.0 GB (raw/uncompressed)