132         outError("Only one state is observed in " + msg);  in checkAbsentStates()
165     if (!ok) outError("Please rename sequences listed above!");  in checkSeqName()
396         outError("Some sequences (see above) are problematic, please check your alignment again");  in checkGappySeq()
442 …      outError("Unknown sequence format, please use PHYLIP, FASTA, CLUSTAL, MSF, or NEXUS format");  in Alignment()
445         outError(ERR_READ_INPUT);  in Alignment()
447         outError(str);  in Alignment()
449         outError(str);  in Alignment()
453         outError("Alignment must have at least 3 sequences");  in Alignment()
493         outError("Alignment must have at least 3 sequences");  in Alignment()
585 		outError("I am confused since both DATA and CHARACTERS blocks were specified");  in readNexus()
590         outError("No DATA or CHARACTERS blocks found");  in readNexus()
645 …outError(data_block->GetTaxonLabel(seq) + " has invalid single state " + ch + " at site " + conver…  in getDataBlockMorphStates()
663         outError("MATRIX command undeclared or invalid");  in extractDataBlock()
667         outError("Continuous characters not supported");  in extractDataBlock()
686         	outError("Number of states can not exceed 32");  in extractDataBlock()
688         	outError("Number of states can not be below 2");  in extractDataBlock()
709 …      outError("MATRIX not found, make sure nexus command before MATRIX ends with semi-colon (;)");  in extractDataBlock()
712         outError("ntax is different from number of matrix rows");  in extractDataBlock()
927         outError(ERR_WRITE_OUTPUT, filename);  in printSiteInfo()
963 		outError("Const pattern frequency vector has different number of states: ", freq_const_patterns);  in addConstPatterns()
970 			outError("Const pattern frequency must be non-negative");  in addConstPatterns()
1399 			outError("Wrong genetic code ", gene_code_id);  in initCodon()
1422 			outError("Wrong genetic code ", gene_code_id);  in initCodon()
1612     	outError("Number of sites is not multiple of 3");  in buildPattern()
2165             outError(str);  in readCountsFormat()
2169 …outError("Custom virtual population size of PoMo not 2, 10 or any other odd number between 3 and 1…  in readCountsFormat()
2193       outError("Multiple sampling methods specified.");  in readCountsFormat()
2200         outError("Abort.");  in readCountsFormat()
2564     if (site_left == -1) outError("Left residue range is too high");  in getSiteFromResidue()
2582             if (seq_id < 0) outError("Reference sequence name not found: ", ref_seq_name);  in buildRetainingSites()
2609             outError(ERR_READ_INPUT, aln_site_list);  in buildRetainingSites()
2611             outError(str);  in buildRetainingSites()
2708             outError("Unspported datatype for NEXUS file");  in printNexus()
2751         outError(ERR_WRITE_OUTPUT, file_name);  in printAlignment()
2954         outError("Cannot convert non-DNA alignment into codon alignment");  in convertToCodonOrAA()
2956         outError("Sequence length is not divisible by 3 when converting to codon sequences");  in convertToCodonOrAA()
3040         outError(err_str.str());  in convertToCodonOrAA()
3054         outError("Cannot convert non-codon alignment into AA");  in convertCodonToAA()
3103         outError("Cannot convert non-codon alignment into DNA");  in convertCodonToDNA()
3245         outError(err);  in extractSiteID()
3247         outError(err);  in extractSiteID()
3258     if (aln->isSuperAlignment()) outError("Internal error: ", __func__);  in createBootstrapAlignment()
3296             outError("Unsupported bootstrap feature, pls contact the developers");  in createBootstrapAlignment()
3300         outError((string)"Unsupported jackknife with sampling " + spec);  in createBootstrapAlignment()
3337 			outError("Sum of lengths exceeded alignment length");  in createBootstrapAlignment()
3360 			outError("Sum of lengths exceeded alignment length");  in createBootstrapAlignment()
3375     		outError("Bootstrap specification length is not divisible by 2");  in createBootstrapAlignment()
3383     			outError("Sum of lengths exceeded alignment length");  in createBootstrapAlignment()
3419         outError((string)"Unsupported jackknife with " + spec);  in createBootstrapAlignment()
3467 			outError("Sum of lengths exceeded alignment length");  in createBootstrapAlignment()
3488 			outError("Sum of lengths exceeded alignment length");  in createBootstrapAlignment()
3502             outError("-bsam not allowed for non-partition model");  in createBootstrapAlignment()
3505 			outError("Bootstrap specification length is not divisible by 2");  in createBootstrapAlignment()
3509 				outError("Sum of lengths exceeded alignment length");  in createBootstrapAlignment()
3564 …if (masked_aln->getNSeq() != aln->getNSeq()) outError("Different number of sequences in masked ali…  in createGapMaskedAlignment()
3565 …if (masked_aln->getNSite() != aln->getNSite()) outError("Different number of sites in masked align…  in createGapMaskedAlignment()
3590         if (seq_id < 0) outError("Masked alignment does not contain taxon ", *it);  in createGapMaskedAlignment()
3609     if (isSuperAlignment()) outError("Internal error: ", __func__);  in shuffleAlignment()
3615     if (getNSeq() != aln->getNSeq()) outError("Different number of sequences in two alignments");  in concatenateAlignment()
3616     if (num_states != aln->num_states) outError("Different number of states in two alignments");  in concatenateAlignment()
3617     if (seq_type != aln->seq_type) outError("Different data type in two alignments");  in concatenateAlignment()
3624         if (seq_id < 0) outError("The other alignment does not contain taxon ", *it);  in concatenateAlignment()
3702         outError("Cannot work with more than 31 states");  in generateSubsets()
3897         outError(ERR_WRITE_OUTPUT, file_name);  in printDist()
3984         outError(str);  in readDist()
3986         outError(str);  in readDist()
3988         outError(ERR_READ_INPUT, file_name);  in readDist()
4078         outError("Alignment file is too short.");  in convertPomoState()
4509         outError("F3X4C not yet implemented. Contact authors if you really need it.");  in computeCodonFreq()
4525         outError("Unsupported codon frequency");  in computeCodonFreq()
4838         outError(ERR_WRITE_OUTPUT, filename);  in printSiteGaps()
4871             outError("Pattern in the current alignment is not found in the reference alignment!");  in multinomialProb()
4887         outError("Error: log likelihood of patterns are not given!");  in multinomialProb()
5121 		outError(str);  in readSiteStateFreq()
5123 		outError(str);  in readSiteStateFreq()
5125 		outError(ERR_READ_INPUT);  in readSiteStateFreq()