30d1e434dcd5b313f393eac770c8da2d4323d54f
angie
  Fri Oct 13 11:45:13 2023 -0700
Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses.
mpxv has been going for over a year, rsv & dengue for some months now.  fluA is an incomplete work in progress,
complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.

diff --git src/hg/utils/otto/rsv/ramaekers.A.clade-mutations.tsv src/hg/utils/otto/rsv/ramaekers.A.clade-mutations.tsv
new file mode 100644
index 0000000..1c9feb1
--- /dev/null
+++ src/hg/utils/otto/rsv/ramaekers.A.clade-mutations.tsv
@@ -0,0 +1 @@
+A18	C215T,A791G,A2856G,C3082A,C5964G,T6076G,C6192G,A6795G,A6999G,T8370A,G10849A > A650C,T651C,A837G,T1054C,G1068A,A1457G,T1646C,C1664T,C2705T,A3023G,T3102C,A3205G,T3222G,T3327C,C4280A,C4517T,A4543G,T4599C,T4724C,T5284C,C5588T,T5590A,T5625C,T5671C,G5733A,G5804A,G6114A,A6746G,T7052C,T7302C,C7577T,C8449T,G9661A,T11800C,T12209G,T12502C,T12679C,T14315C,G14539A > T194C,C702T,A740G,A1001G,T1015G,C1041T,T3124A,A3135C,C3533N,A3566G,T3677A,T4053A,C4152T,T4175C,T4289G,T4555C,G4799A,C4899T,T4987C,C4988T,C4989T,T4993N,C4998T,T5019C,T5104C,G5157A,T5351C,A5428G,T5491C,C5573A,A5706G,C5822T,G6024A,T6584A,C7148T,A7343G,G7449A,G7562A,A7653G,C7869T,G7944A,A8350C,T8440C,C8445T,C8462A,T8486C,A8992G,G9076A,C9124T,C9192T,C9238T,A9830G,C9869T,C10168T,A10174G,G10757A,C10825T,A10958G,G11305A,C11348T,C11506T,T11857C,A11956G,G12067A,T12196A,C12337T,G12472A,C13519T,T13815C,C13849T,C13891T,C13927T,T14017C,C14035T,G14371A,T14403C > A30G,T527A,A580G,C639A,G687A,A846G,C915T,T966C,A1029G,C1033T,T1052C,T1110C,A1118G,G1119A,G1139A,G1349T,G1358A,A1424G,A1631G,C1682T,C1730T,C1751N,C1785T,C1790T,A1922G,T1961C,T1994G,T2027A,G2147A,G2162A,A2186T,C2241T,G2393A,T2528C,C2534A,C2563T,A2621G,T2642A,C2693T,G2807A,T2919C,T3086G,C3132T,T3136C,C3153N,A3226C,G3250A,G3281A,T3386C,C3468T,T3536C,A3563G,G3665A,T3686C,T3689C,C3713T,A3863G,C3977A,A4057G,C4095A,C4100T,A4107C,A4111C,A4147G,A4213C,T4265C,A4285G,G4293A,T4434C,T4471C,T4504C,A4511G,A4539G,A4540T,C4554T,C4568A,T4572A,T4576C,C4583T,A4594G,C4598T,G4648A,C4654T,T4717C,T4754C,T4972C,T5007C,G5048A,A5050T,C5109T,A5269T,C5309A,T5347A,G5384A,T5418G,T5460A,T5472A,T5480C,T5518A,C5526A,C5544T,T5555C,C5564T,C5576A,T5586C,A5595G,A5597G,C5604T,A5605G,C5623A,A5641C,G5682A,C5705T,T5718C,T5720C,T5732C,A5969C,T6077C,A6266G,T6308C,A6311T,C6410T,G6434A,A6539G,A6641G,T6671C,T6809C,G6810A,T6839C,A6995G,C7022T,T7310C,C7580T,T7764C,T7824C,T7827C,T7926C,T7935C,T7964C,C8127T,T8160C,C8211A,A8233T,C8289A,G8302A,A8318C,C8359T,A8360G,T8394C,G8398T,T8407C,G8458A,T8460C,T8471C,G8488A,C8566T,G8578A,G8674A,T8738A,G8807A,A8890G,G8905A,C8982T,C9046T,A9168G,G9187T,A9208T,T9223C,C9370T,G9463A,C9761T,T9841N,T10009C,G10042T,T10105C,A10117G,C10189T,T10252C,C10318T,G10396A,G10411A,G10423A,C10546T,G10633A,G10654A,C10816T,C10951T,C11017T,C11087A,C11312T,T11318C,A11440G,C11566T,T11755C,T11794C,A11923C,C12035T,G12043A,T12223C,C12433T,C12445T,A12463G,C12499T,A12571T,C12589T,C12643T,A12934G,A12940G,A13030G,T13081C,T13144C,A13149G,C13174T,T13186C,A13279G,T13322C,C13466T,G13639A,G13649A,A13658G,G13763A,C13810T,G13830A,C13864T,C13888T,C14107T,C14308T,A14350G,T14437C,G14506T,G14509A,A14543G,A14545G,A14620G,C14869T,C14902T,C14969T,G15004A,T15032C,C15076T,G15117A,A15128G,T15133A,C15151T,T15154A,G15175A,T15187C > C88T,G263A,A317G,C345T,T389C,T407C,C411A,T612C,T1028C,A1574G,C3157T,A3171C,C3179A,T3824C,A4698C,A5054G,T5726C,T5879C,G6158A,A6608G,C6977T,T7289A,A7384G,T7422C,C7431A,T7432C,G7533T,C7773T,G7947A,T8109C,A9085G,A11701G,A11743T,G12118A,T14455C,A14821G,A15063T > C589T,A619N,A2810G,A7483C,A7592G,G9216A,A9562G > C2102T > A137G,T506C,T1232C,T1235C,T1241C,T1278C,G1390A,G1487A,G2192A,A2765G,T3076C,C3344T,C3596T,C3827T,T4258C,C4287T,C4374A,T4563C,T4608C,A5018C,G5065A,C5579T,T6659C,A6752G,A6950G,C7004T,C7340T,C7439T,C7470T,T8364C,A9166T,A9349G,G11374A,A12427G,C12514T,T12739C,A13788G,A14653G,A14713T,A15072T,A15089N,T15098C > T8584C,A10759G > C1021A,C1051T,T2000G,T4437C,C4823T,T5002C,T5052C,C5053T,T5064C,C5364T,A6794G,C7488T,T10066A,G10141A,T11116C > A3290G,C5116T,C5552T,T6119C,T6215C,C9434T,G11692A,C14858T > T4141C,C13672T > G3248A,C3428T,T4145N,T4184C,C4286T,C6242T,C6596T,G7407A,G7482A,C8542T,C9406T > T110C,T206G,G233T,C738T,A960T,T969A,C1010A,A1409T,T2396C,T2399C,C3095A,C3108T,A3161G,C3164T,T3464C,T3605C,G4236A,A4237G,A4549T,C4603T,T4660C,T4666C,C4819T,G4929A,C5154A,T5492A,C5556T,A5690T,G5999A,A6032C,C7166T,C7187A,C7301T,A7381G,A8157G,G8260A,T8273A,A9144G,T9955C,T10216C,C10219T,C10459T,T10462C,A10792G,G10876A,A11113G,T11344C,A11818T,T12037A,T12241C,C12908A,C13117A,C13516T,A13596G,A13686G,T14158A,C14386T,T14900C,T15000C > C2542T,T5515N,T6920C > T144C,T521C,A714T,A1090T,A1412G,G1970A,A2015G,C2175T,A2591G,T3083A,G3113A,C4291T,A4323T,C4393A,G5122A,C5578A,A5580G,A5602G,A6206T,C6530A,C6713T,C7097T,T7178C,G7259A,C7428T,A7978G,G8232A,A8514G,T8755C,C8812T,A8854C,T8896C,G8956T,T8989C,T9469C,A9700G,T10043C,T10450A,G10758A,C11047A,A11662T,C12421T,A12553T,G13003T,A13240G,T13731C,A14029G,A14338G,C14717T,C14984A,A14999G,G15137A,A15144G > A161G,C840T,T1274C,C1745T,C2438T,T3151C,C3197T,A3353G,C4498T,T4501C,C5015A,C5140T,C5442T,G5448A,C5454A,A5681G,A5960G,A5967T,A6677G,A7106T,A7263G,T7364C,C7447T,C7551A,A7552C,C8088A,T8213A,C9752T,A9880G,T10264C,A10939T,T11461C,T12640A,G13156A,C13157T,G13732A,T14575C,T15110C,G15134A