diff --git a/src/msta_scores.cpp b/src/msta_scores.cpp
index a2a5b8d..e3389cd 100644
--- a/src/msta_scores.cpp
+++ b/src/msta_scores.cpp
@@ -21,11 +21,11 @@ void cmd_msta_scores()
 
 	const bool DoCore = opt_core;
 
-	string LabelDir;
-	if (optset_labeldir)
+	string SeqsDir;
+	if (optset_seqsdir)
 		{
-		LabelDir = string(opt_labeldir);
-		Dirize(LabelDir);
+		SeqsDir = string(opt_seqsdir);
+		Dirize(SeqsDir);
 		}
 
 	const uint N = SIZE(Accs);
@@ -45,18 +45,12 @@ void cmd_msta_scores()
 			}
 
 		SeqDB MSA;
-		if (optset_labeldir)
+		if (optset_seqsdir)
 			{
-			set<string> EvalLabels;
-			vector<string> EvalLabelVec;
-			string LabelFN = LabelDir + Acc;
-			ReadLinesFromFile(LabelFN, EvalLabelVec);
-			uint N = SIZE(EvalLabelVec);
-			if (N == 0)
-				Die("Empty -labels file");
-			for (uint i = 0; i < N; ++i)
-				EvalLabels.insert(EvalLabelVec[i]);
-			MSA.FromFasta_Labels(FN, EvalLabels, true);
+			string SeqsFN = SeqsDir + Acc;
+			SeqDB EvalSeqs;
+			EvalSeqs.FromFasta(SeqsFN, false);
+			MSA.FromFasta_Seqs(FN, EvalSeqs, true);
 			}
 		else
 			MSA.FromFasta(FN, true);
diff --git a/src/myopts.h b/src/myopts.h
index ca99ba8..b68143b 100644
--- a/src/myopts.h
+++ b/src/myopts.h
@@ -59,7 +59,7 @@ STR_OPT(scoredist)
 STR_OPT(ref)
 STR_OPT(label)
 STR_OPT(labels)
-STR_OPT(labeldir)
+STR_OPT(seqsdir)
 STR_OPT(fasta)
 STR_OPT(feature_fasta)
 STR_OPT(alnout)
diff --git a/src/seqdb.cpp b/src/seqdb.cpp
index 5c938e9..e17bbf3 100644
--- a/src/seqdb.cpp
+++ b/src/seqdb.cpp
@@ -163,36 +163,49 @@ void SeqDB::SetIsNucleo()
 	m_IsNucleoSet = true;
 	}
 
-void SeqDB::FromFasta_Labels(const string &FileName,
-  const set<string> &Labels, bool AllowGaps)
+void SeqDB::FromFasta_Seqs(const string &FileName,
+  const SeqDB &EvalSeqs, bool AllowGaps)
 	{
 	SFasta SF;
 	SF.Open(FileName);
 	SF.m_AllowGaps = AllowGaps;
 	uint FoundCount = 0;
 	m_IsAligned = false;
+	set<string> EvalSeqSet;
+	const uint EvalSeqCount = EvalSeqs.GetSeqCount();
+	for (uint i = 0; i < EvalSeqCount; ++i)
+		EvalSeqSet.insert(EvalSeqs.GetSeq(i));
+
 	for (;;)
 		{
 		const char* Seq = SF.GetNextSeq();
 		if (Seq == 0)
 			break;
-		const string Label = SF.GetLabel();
-		if (Labels.find(Label) == Labels.end())
-			continue;
-		++FoundCount;
 		const unsigned L = SF.GetSeqLength();
 		if (L == 0)
 			continue;
+		const string Label = SF.GetLabel();
+
+		string s2;
+		for (uint i = 0; i < L; ++i)
+			{
+			char c = Seq[i];
+			if (!isgap(c))
+				s2 += toupper(c);
+			}
+		if (EvalSeqSet.find(s2) == EvalSeqSet.end())
+			continue;
+
+		++FoundCount;
 		string s;
 		for (unsigned i = 0; i < L; ++i)
 			s.push_back(Seq[i]);
 		AddSeq(Label, s);
 		}
-	const uint LabelCount = SIZE(Labels);
 	if (FoundCount == 0)
 		Die("No labels found");
-	if (FoundCount < LabelCount)
-		Warning("%u / %u labels not found", LabelCount - FoundCount, LabelCount);
+	if (FoundCount < EvalSeqCount)
+		Warning("%u / %u labels not found", EvalSeqCount - FoundCount, EvalSeqCount);
 	}
 
 void SeqDB::FromFasta(const string& FileName, bool AllowGaps)
diff --git a/src/seqdb.h b/src/seqdb.h
index 7c55264..f9b37f6 100644
--- a/src/seqdb.h
+++ b/src/seqdb.h
@@ -42,7 +42,7 @@ class SeqDB
 	bool GetIsNucleo();
 	unsigned GetSeqCount() const { return SIZE(m_Seqs); }
 	void FromFasta(const string &FileName, bool AllowGaps = false);
-	void FromFasta_Labels(const string &FileName, const set<string> &Labels, bool AllowGaps = false);
+	void FromFasta_Seqs(const string &FileName, const SeqDB &Seqs, bool AllowGaps = false);
 	void WritePretty(FILE *f) const;
 	void LogMe() const;