Sorry, wrong version, the code I meant to post was:

#!/usr/bin/perl

$fileName = "tmp.txt";

open(CPF, $fileName) or die ("Can't open file ", $fileName);
@lines = <CPF>;
close (CPF);

$index = 0;
@allNames;
@allSeq;
$nbTaxa;
$nbGenes;
#$lastLine = "start";        

$alternatingIter = sub {return $_[0]};
$followedIter = sub {return (($_[0] % 10) - 1) };
$iter;


chop $lines[0];
($nbTaxa,$nbGenes)=split / +/, $lines[0];    
print $nbTaxa." ".$nbGenes."\n";


&sorter ($lines[1]);

($first, $second)= split / +/, $lines[2];

if (((length $second) == 0) && ($first =~ /[AGTC]+/)){    
    $iter = $followedIter;
    chop ($first);
    $allSeq[$index]= $allSeq[$index].$first;

    print "TYPE: just sequence  -->  ";
    print "first:".$first.";  second:".$second.";\n";
}


elsif (((length $second) > 0) && ($first =~ /(\w)+/) &&  ($second =~ /
+[AGTC]+/) ){    
    $iter = $alternatingIter;
    $allNames [$index] = $first;
    chop ($second);
    $allSeq [$index] = $second;
    $index++;

    print "TYPE: name + sequence -->  ";
    print "first:".$first.";  second:".$second.";\n";
    }

foreach $tmp (@lines[3..@lines]){
    &sorter ($tmp, $iter);
}

for ($i = 0; $i <= $index; $i++){
    print $allNames[$i]." -->  ".$allSeq[$i]."\n";
}

sub sorter {
    my $tmp = $_[0];
    my $iter = $_[1];
    ($first, $second)= split / +/, $tmp;

    if (((length $second) == 0) && ($first =~ /[AGTC]+/)){
        chop ($first);
        $allSeq[$iter]= $allSeq[$index].$first;
        $index++;

        print "TYPE: just sequence  -->  ";
        print "first:".$first.";  second:".$second.";\n";
    }


    elsif (((length $second) > 0) && ($first =~ /(\w)+/) &&  ($second 
+=~ /[AGTC]+/) ){
        $i = &{$iter}($index);    # ou $iter->($index);
        $allNames [$i] = $first;
        chop ($second);
        $allSeq [$i] = $second;
        $index++;

        print "TYPE: name + sequence -->  ";
        print "first:".$first.";  second:".$second.";\n";
    }
    elsif($first eq "\n"){
        print "TYPE: do nothing -->  ";
        print "first:".$first.";  second:".$second.";\n";
    }
    else{
        print "TYPE: you have a problem with the format of file".$file
+Name." -->  ";
        print "first:".$first.";  second:".$second.";\n";
    }
    print "index: ".$index."\n";
}
[download]

Here is the tmp.txt file you should use as input

10  705
Cow       ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTA
Carp      ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT
Chicken   ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC
Human     ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTT
Loach     ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTT
Mouse     ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTA
Rat       ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTT
Seal      ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTA
Whale     ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTC
Frog      ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTA

CTTCACTTTCATGACCACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTAC
CTTCACTTCCACGACCACGCATTAATAATTGTGCTCCTAATTAGCACTTTAGTTTTATAT
GTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTAC
ATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTAT
CTTCACTTCCATGACCATGCCCTAATAATTGTATTTTTGATTAGCGCCCTAGTACTTTAT
ATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTAT
ACAAACTTTCATGACCACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTAT
CTACACTTCCATGACCACACATTAATAATTGTGTTCCTAATTAGCTCATTAGTACTCTAC
CTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTAC
CTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTAC
[download]