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JAL-4394
The 'alignment' option has become unclickable
Some ensembl queries may not work reliably in 2.11.3.0, 2.11.4.0
Jalview service
Alignment not working for multiple sequences. A window is appearing saying "Invalid JABA URLs in your web service preference"
Jalview 2.11.2.5 not compatible with 3d-beacons api v2.0
PFAM services have a new certificate that JRE cacerts does not cover
Annotation web services do not add annotations in JalviewJS
Edit web service parameters dialog does not work in jalviewjsJAL-3807
Migrate Jalview JPred Client to use Slivka's JPred Services
Intermittent errors when running AACon
JPred prediction for a sequence with start position greater than one is offset when added to a new view via 'Add Reference Annotation'
don't have full access to the software.JAL-2707
Ensembl / EnsemblGenomes id resolution at scale
Jalview cannot connect to a JABAWS 2.2 virtual machine
Exception while querying Uniprot via the REST API
Fetch DBRefs from EMBL gives Illegal Text data found as child of: ROOT
(unannounced) changes to ENA 1.2 XML format
EnsemblGenomes queried with non-existent identifier takes a long time to report 'not found'
BioJS export fails when BioJS templates can't be downloaded
External service integration test for the PDB Solr API
Problem connecting to Jabaws
Web Service Connection Problem
jnet job queues forever if a very short sequence is submitted for prediction
CAth das server errors appear as features in the alignment
Muscle web service gives very poor alignment result
Job submission and result retrieval fails and server error logs fill with 'Too many open files' Exceptions
broken job statistics are under-estimates
WsDBFetch client fails on jon Manning's vaioJAL-259
Log number and reason for jobs being killed due to exhaustion of allocated job resources
JNet error state not detected (blastpgp failure)
Scheduler killing jobs is logged as broken job
Web Service Job Status and Service Availability
Web Service Input Data Validation
errors due to jobs disk being full are not logged locally
JNet server code does not verify valid input to service
Empty Sequence In Multiple Sequence Alignment Submission
MuscleWS translates selenomethionine 'U' to unknown residue 'X'
Uracils in sequence alignment are not detected when a jnet job is submitted
Memory efficiency for SOAP Messages
JPred Client submission of MSA leads to HMMER error
JPred Client would hang after completion of jobs where homologs had non-unique Sequence IDs
Uniprot/SwissProt name inconsistencies.
EBI uniprot record PDB database reference format changed
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