MuscleAlignmentDialog Align with MUSCLE Align with MUSCLE Input and output Input and output Input file Input file ... ... Output file Output file Mode Mode Mode details: Mode details: Advanced options Advanced options Max iterations Max iterations Max time (minutes) Max time (minutes) Translating alignment to amino allows to avoid errors of inserting gaps within codon boundaries. Translating alignment to amino allows to avoid errors of inserting gaps within codon boundaries. Translate to amino when aligning Translate to amino when aligning Translation table: Translation table: Region to align Region to align - - Whole alignment Whole alignment Column range Column range Do not re-arrange sequences (-stable) Do not re-arrange sequences (-stable) QObject Region should be set as 'start..end', start should be less than end, e.g. '1..100' Region should be set as 'start..end', start should be less than end, e.g. '1..100' U2::LocalWorkflow::MusclePrompter from %1 from %1 Aligns each MSA supplied %1 with MUSCLE using "%2" mode. Aligns each MSA supplied %1 with MUSCLE using "%2" mode. U2::LocalWorkflow::MuscleWorker Input MSA Input MSA Multiple sequence alignment Multiple sequence alignment Mode Mode Stable order Stable order Maximum number of iterations. Maximum number of iterations. An empty MSA '%1' has been supplied to MUSCLE. An empty MSA '%1' has been supplied to MUSCLE. Multiple sequence alignment to be processed. Multiple sequence alignment to be processed. Result of alignment. Result of alignment. Max iterations Max iterations Region to align Region to align Whole alignment or column range e.g. 1..100. Whole alignment or column range e.g. 1..100. Align with MUSCLE Align with MUSCLE MUSCLE is public domain multiple alignment software for protein and nucleotide sequences.<dfn>MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation.</dfn> MUSCLE is public domain multiple alignment software for protein and nucleotide sequences.<dfn>MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation.</dfn> Region end position should be greater than start position Region end position should be greater than start position Aligned %1 with MUSCLE Aligned %1 with MUSCLE Selector of preset configurations, that give you the choice of optimizing accuracy, speed, or some compromise between the two. The default favors accuracy. Selector of preset configurations, that give you the choice of optimizing accuracy, speed, or some compromise between the two. The default favors accuracy. Do not rearrange aligned sequences (-stable switch of MUSCLE). Otherwise, MUSCLE re-arranges sequences so that similar sequences are adjacent in the output file. This makes the alignment easier to evaluate by eye. Do not rearrange aligned sequences (-stable switch of MUSCLE). Otherwise, MUSCLE re-arranges sequences so that similar sequences are adjacent in the output file. This makes the alignment easier to evaluate by eye. U2::LocalWorkflow::ProfileToProfileTask Align profile to profile with MUSCLE U2::LocalWorkflow::ProfileToProfileWorker Aligned profile to profile with MUSCLE Aligned profile to profile with MUSCLE Master profile Master profile The main alignment which will be aligned on. The main alignment which will be aligned on. Second profile Second profile Alignment which will be aligned to the master alignment. Alignment which will be aligned to the master alignment. Align Profile to Profile With MUSCLE Align Profile to Profile With MUSCLE Aligns second profile to master profile with MUSCLE aligner. Aligns second profile to master profile with MUSCLE aligner. U2::MuscleAdapter No sequences in input file No sequences in input file Internal MUSCLE error: %1 Internal MUSCLE error: %1 Undefined internal MUSCLE error Undefined internal MUSCLE error Alignment is empty Alignment is empty Invalid input alignment Invalid input alignment Incompatible alphabets Incompatible alphabets Aligning profiles Aligning profiles Building output Building output Aligning sequence %1 of %2 Aligning sequence %1 of %2 Merging results: %1 of %2 Merging results: %1 of %2 Not enough memory to do this alignment. You can try the 64-bit version of UGENE. In this case, more available memory will be used for aligning. Not enough memory to do this alignment. You can try the 64-bit version of UGENE. In this case, more available memory will be used for aligning. Not enough memory to do this alignment. Not enough memory to do this alignment. Unsupported alphabet: %1 Unsupported alphabet: %1 U2::MuscleAddSequencesToProfileTask MUSCLE align profiles '%1' vs '%2' MUSCLE align profiles '%1' vs '%2' MUSCLE align '%2' by profile '%1' MUSCLE align '%2' by profile '%1' A problem occurred during aligning profile to profile with MUSCLE. The original alignment is no more available. Sequences in file have different alphabets %1 Sequences in file have different alphabets %1 No sequences found in file %1 No sequences found in file %1 No alignment found in file %1 No alignment found in file %1 U2::MuscleAlignDialogController Error Error Illegal alignment region Illegal alignment region Align Align Cancel Cancel MUSCLE default MUSCLE default The default settings are designed to give the best accuracy The default settings are designed to give the best accuracy Command line: muscle <no-parameters> Command line: muscle <no-parameters> Large alignment Large alignment If you have a large number of sequences (a few thousand), or they are very long, then the default settings may be too slow for practical use. A good compromise between speed and accuracy is to run just the first two iterations of the algorithm If you have a large number of sequences (a few thousand), or they are very long, then the default settings may be too slow for practical use. A good compromise between speed and accuracy is to run just the first two iterations of the algorithm Command line: muscle -maxiters 2 Command line: muscle -maxiters 2 Refine only Refine only Improves existing alignment without complete realignment Improves existing alignment without complete realignment Command line: muscle -refine Command line: muscle -refine U2::MuscleAlignWithExtFileSpecifyDialogController Align Align Cancel Cancel Open an alignment file Open an alignment file Save an multiple alignment file Save an multiple alignment file Error Error Illegal alignment region Illegal alignment region Kalign with Align Align with Kalign Input file is not set! Input file is not set! Output file is not set! Output file is not set! U2::MuscleGObjectRunFromSchemaTask Workflow wrapper '%1' Workflow wrapper '%1' MUSCLE align '%1' MUSCLE align '%1' MUSCLE refine '%1' MUSCLE refine '%1' U2::MuscleGObjectTask MUSCLE align '%1' MUSCLE align '%1' MUSCLE refine '%1' MUSCLE refine '%1' MUSCLE add to profile '%1' MUSCLE add to profile '%1' MUSCLE align profiles MUSCLE align profiles MultipleSequenceAlignment object has been changed MAlignment object has been changed MAlignment object has been changed U2::MuscleMSAEditorContext Align with MUSCLE... Align with MUSCLE... Align sequences to profile with MUSCLE... Align sequences to profile with MUSCLE... Align profile to profile with MUSCLE... Align profile to profile with MUSCLE... Select file with sequences Select file with sequences Select file with alignment Select file with alignment U2::MuscleParallelTask MuscleParallelTask MuscleParallelTask There is not enough memory to align these sequences with MUSCLE. U2::MusclePlugin MUSCLE MUSCLE A port of MUSCLE package for multiple sequence alignment. Check http://www.drive5.com/muscle/ for the original version A port of MUSCLE package for multiple sequence alignment. Check http://www.drive5.com/muscle/ for the original version Align with MUSCLE... Align with MUSCLE... U2::MusclePrepareTask Preparing MUSCLE alignment... Preparing MUSCLE alignment... Internal parallel MUSCLE error: %1 Internal parallel MUSCLE error: %1 MUSCLE prepared successfully MUSCLE prepared successfully No sequences in input file No sequences in input file Alignment is empty Alignment is empty U2::MuscleTask MUSCLE alignment MUSCLE alignment MUSCLE alignment started MUSCLE alignment started Incorrect region to align Incorrect region to align Stopping MUSCLE task, because of error in MultipleSequenceAlignment::mid function Stopping MUSCLE task, because of error in MAlignment::mid function Stopping MUSCLE task, because of error in MAlignment::mid function Performing MUSCLE alignment... Performing MUSCLE alignment... MUSCLE alignment successfully finished MUSCLE alignment successfully finished Unexpected number of rows in the result multiple alignment! Unexpected number of rows in the result multiple alignment! U2::ProgressiveAlignTask ProgressiveAlignTask ProgressiveAlignTask Internal parallel MUSCLE error: %1 Internal parallel MUSCLE error: %1 alignment "%1" Parallel MUSCLE Iter 1 accomplished. Time elapsed %2 ms alignment "%1" Parallel MUSCLE Iter 1 accomplished. Time elapsed %2 ms U2::ProgressiveAlignWorker ProgressiveAlignWorker ProgressiveAlignWorker Internal parallel MUSCLE error: %1 Internal parallel MUSCLE error: %1 U2::RefineTask RefineTask RefineTask Internal parallel MUSCLE error: %1 Internal parallel MUSCLE error: %1 Can't allocate enough memory to perform aligning, try to use 64bit UGENE version U2::RefineTreeTask RefineTreeTask RefineTreeTask Internal parallel MUSCLE error: %1 Internal parallel MUSCLE error: %1 U2::RefineWorker Internal parallel MUSCLE error: %1 Internal parallel MUSCLE error: %1 Can't allocate enough memory to perform aligning, try to use 64bit UGENE version